Academic Year 2024-2025
1-5 September, Bio3 Forum, register here
10 September, 12 pm, IS2, Eliza mock exam, "Structural and dynamical studies of K- Ras4BG12D dimers using Molecular Dynamics simulations"
18 September, 9am, Eliza MSc exam, "Structural and dynamical studies of K- Ras4BG12D dimers using Molecular Dynamics simulations"
23 September, online, 10am, Maria mock exam "Using deep learning and natural language processing to predict protein allosteric sites"
24-27 September, CECAM workshop on "Understanding Peripheral Protein-Membrane Interactions". Free registration for online participation.
25-28 September, Panhellenic Chemistry Conference
16 October, Nastazia, 10am, IS2 "Studying the dimerization of KRAS-4B"
21 October Francho, 2pm "Development of a computational methodology to detect allosteric pathways in proteins and application in drug discovery"
22 October, 3pm, online, Maria Mamai thesis exam, "Using deep learning and natural language processing to predict protein allosteric sites"
11 November, 2.30 pm IS2, Danai, "Investigating the protein-membrane interface of peripheral membrane proteins using molecular simulations"
2 December, 2.30pm IS2, Matilde, "Exploring RNA-Small Molecule Interactions via Alchemical Transformations: A Case Study on HIV-1 Trans-Activation Response RNA"
9 December, 3pm IS2, Sotiris, "Predicting protein-membrane interfaces of peripheral membrane proteins using machine learning techniques"
TBA Panos, "Studying the dimerization of KRAS-4B"
TBA, Stevi, "Molecular Dynamics simulations and computer-aided drug design for PTEN"
TBA, Vassilis, "Predicting the 3D structure of RNA"
Christmas Break
Academic Year 2023-2024
4 September, 5 pm, IS2, Giannis mock exam, "Using Deep Learning to predict three-dimensional RNA structure"
5 September, 2pm, Biology Department, Giannis thesis presentation, "Using Deep Learning to predict three-dimensional RNA structure"
14 September, 11am, Francho
29 September, 1pm, Lefteris Mainas, Brown University, "Large-Deviation Theory Approach to Systems with Orientational Order: Results for Two and Three Dimensional Liquid Crystals"
29 September, Researchers Night
10-12 October Athens Science Festival
2 November, 3pm IS2, Panos "Martini 3 force field parameters for protein lipidation post-translational modifications"
16 November, 3pm IS2, Danai "Insights into the C-terminal activation and protein-membrane interface of PI3Kα using molecular simulations"
4 December, 3pm IS2, Eliza, "Molecular Dynamics simulations and computer-aided drug design targeting K-Ras4B"
Christmas Break
10 January, 10am, IS2, Francho, "Development of a computational methodology to detect allosteric pathways in proteins and application in drug discovery"
22 January, 3pm IS2, Stevi, "Molecular Dynamics simulations and computer-aided drug design for PTEN"
7 February, 2-4pm, Molecular Modeling Class Exam (teleconference room)
13 February, 1pm, online, Danai, "Investigating the protein-membrane interface of peripheral membrane proteins using molecular simulations"
19 February, 3pm, IS2, Vassilis, "Predicting the 3D structure of RNA"
26 February, 12pm, IS2, Nastazia, "Studying the dimerization of KRAS-4B"
11 March, Stevi "Molecular Dynamics simulations and computer-aided drug design for PTEN"
9 April, 3pm, IS2, Panos, "Studying the dimerization of KRAS-4B"
17 April, 10 am online, Muhammad "Results from the rotation "Molecular Modeling of Biomolecules"
18-19 April, Athens Science Festival
Easter break
19-23 May ISQBP President's meeting
28 May, 11am, IS2, Ruben Abagyan, University of California, San Diego, USA "Drugs ex machina at blazing GPU speed."
3 June, Ioanna Ilie, 12pm IS1, "Cracking the code: A computational expedition into the neurodegenerative polypeptides and innovative therapies"
Summer Break
Academic Year 2022-2023
21-22 September, Virtual Workshop on Free Energy Methods in Drug Design.
30 September, 10 am, online, Celia mock exam, "Υπολογισμοί διατάραξης ελεύθερης ενέργειας για τη μελέτη πρόσδεσης νευροτοξινών στο γλουταμινικό υποδοχέα ΑΜΡΑ"
30 September, 1 pm, online, Klea mock exam, "Αξιολόγηση της σταθερότητας συμπλόκων του ογκογονιδίου c-Myc και πιθανών αναστολέων μέσω προσομοιώσεων Μοριακής Δυναμικής"
4 October, 1 pm online, Celia exam "Υπολογισμοί διατάραξης ελεύθερης ενέργειας για τη μελέτη πρόσδεσης νευροτοξινών στο γλουταμινικό υποδοχέα ΑΜΡΑ"
6 October, 3.30 pm, online, Klea mock exam, "Αξιολόγηση της σταθερότητας συμπλόκων του ογκογονιδίου c-Myc και πιθανών αναστολέων μέσω προσομοιώσεων Μοριακής Δυναμικής"
19 October, ΙΣ1, 4pm Michalis, Modeling the glycosylated state of the spike protein variants on a model cell membrane
21 October, 6 pm, Prof. Rommie Amaro, "In situ dynamics reveal unseen vulnerabilities of viral glycoproteins" (Department of Chemistry and Biochemistry, University of California, San Diego). Register here: https://www.mgms.org/WordPress/lecture-tour/
24 November, 2 pm Danai, Modeling the active state of PI3Ka
28 November, Alexis, 4 pm, IS1 Using adaptive sampling simulations to study K-RAS dimerization
1 December, 1 pm, Ioannis Papazoglou, IS1 "Using Deep Learning to predict the 3D structure of RNA"
5 December, 2 pm Panos, IS2
12 December, 2 pm Dimitra Paranou, ΙΣ2, "Using deep learning to predict protein-membrane interactions for peripheral membrane proteins"
14 December, 12 pm Maria Mamai, Γ2, "Using deep learning to predict protein allosteric sites"
Christmas Break
30/1, 3 pm, Maria Mamai, IS2, "Using deep learning to predict protein allosteric sites"
14/2, 2 pm, Teleconference room, Final presentations by students of "Molecular Modeling of Biomolecules" 2021-2022 Class.
3/3, 2 pm, Francho, IS2, "AlloViz: a Python package for network-based modelling of protein allostery"
9/3, 4 pm, Francho, IS2, "Development of a computational methodology to detect allosteric pathways in proteins and application in drug discovery"
20/3, 11 am, IS2, Dimitra, "Using deep learning to predict protein-membrane interactions of peripheral membrane proteins""
23/3, 4 pm, online: Zoe "CECAM Mixed-Gen Season 3 – Session 5: Data science in biophysics for applications to drug discovery. Zoom link will appear here: https://www.cecam.org/workshop-details/1187
24/3, 4 pm, Francho, (online) Journal Club: "Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations."
27/3, 11 am, Giannis, IS2, "Sequence to Structure: predicting RNA 3D shape using Evolutionary Information acquired from Nucleic Acid language models"
31/3, 11 am Martijn, IS2, "Searching for cryptic allosteric sites using enhanced sampling methods"
5/4, 3 pm, Simone, Γ2, "Allosteric drugs development for receptor mosaics"
Easter break
26/4, 1 pm, Dimitra, Teleconference room, Master's thesis defense: "Using deep learning and natural language processing to predict protein-membrane interactions of peripheral membrane proteins"
18/5 1pm Giannis, IS2, "Sequence to Structure: predicting RNA 3D shape using Evolutionary Information acquired from Nucleic Acid language models"
19/6 Danai, 2pm IS2, "Insights into the mechanism of the C-terminal PIK3CA activating mutations"
22/6 Lexane, 4pm, IS2 "Toward a streamlined approach to identify and characterize allosteric antibodies"
10/7 Nastazia Lesgidou, 12pm, IS2, "Understanding the conformational differences between TYK2 and its protective polymorphism through Long-range molecular dynamics "
Summer Break
Academic Year 2021-2022
"September 2, 2.30pm, Sébastien Hoyas, Université de Mons, Belgium, "Characterization and Exploitation of Peptoid Secondary Structures: A Synergistic Experimental and Computational Approach"
September 16, 2pm, Jon, "Proton mediated enzyme communication and catalysis".
September 20, 3pm, Melina, "Ανάλυση κοιλοτήτων πρόσδεσης της ογκοπρωτεΐνης KRAS-4B με Μοριακές Δυναμικές προσομοιώσεις"
September 30, 3pm, Eleftheria, "Μοριακές Δυναμικές προσομοιώσεις του διμερισμού της ογκοπρωτεΐνης KRAS-4B"
October 7, 3pm, Group gathering, start of the semester
October 14, 3pm, Zoi, IS2, "Theoretical Study of Cyanotoxin Degradation: Background and Preliminary studies"
October 21, 2pm, Panagiotis Koukos, Utrecht University, "Perspectives on biomolecular simulation: From MD to Docking"
November 15, 2pm, Alexis, "Investigating allosteric networks in proteins using computational methods"
November 18-19, 3-8pm, "Online Conference of the European Chemical Society, Theoretical and Computational Division"
December 1, 3 pm, Panos "Shape-restrained modelling of protein-small molecule complexes with HADDOCK."
December 3, 10.30 am, Sofia, "Adaptive Sampling Simulations and Markov State Modeling"
December 13, 10.30 am, Danai, "Understanding how kinase domain mutations of PI3Kα alter lipid kinase activity using Molecular Dynamics simulations"
December 17, 12 pm, Michalis
Christmas Break
January 18, 3 pm, Danai, zoom meeting, "Allostery in Membrane Proteins"
January 26, 3 pm, Isidora, zoom meeting, Investigation of BMAA and its carbamate adducts as potential inhibitors of
the glutamate receptor AMPA using MD/FEP calculations
February 3, 4 pm, Danai, zoom, "Allostery in Membrane Proteins"
February 15, 2-5pm, ΙΣ2, Final presentations by students of "Molecular Modeling of Biomolecules" 2021-2022 Class.
February 17, 5 pm, Danai, zoom, "Investigating the protein-membrane interface"
February 23, 2.30 pm, Danai "Investigating the protein-membrane interface"
February 24, 6pm, 10th EFMC-YSN MedChemBioOnline: What Can the Medicinal Chemists Learn from Data Sciences?
March 3, 6.15pm, online, Prof. Xavier Barril, "Robustness of protein-ligand complexes: Applications in structure-based virtual screening", The online stream will be provided here.
March 10, 4 pm, Alexis PhD thesis mock exam
Easter Break
May 4, 16:05AM - 16:35 "Rapid Discovery of Potent Inhibitors of the Main Protease of SARS-CoV2", William Jorgensen (Yale University)Register here: https://t.co/w0RCjjraQ4
May 5, 5-6.30pm,
"Everything You Wanted to Know About Alchemical Free Energy Calculations But Were Afraid to Ask"Antonia Mey, University of Edinburgh
"Applications and Impact of Binding Free Energy Calculations in Drug Discovery"
Christina Schindler, Merck Healthcare KGaA
Register here: https://zoom.us/meeting/register/tJAvce-hqzIoH9DFjvlpKKmHbhNMTXtUkcWi
May 12, 4pm, Valery Lutsyk, "Extending the MARTINI 3 Coarse-Grained Force Field to Carbohydrates".
May 30, 3pm, Klea, ΙΣ2, Investigating the structure and dynamics of Myc inhibitors of the oncoprotein Myc
May 26, 4pm, Celia ΙΣ2, "Free Energy Perturbation calculations to study neurotoxic binding on the AMPA receptor".
June 2, 4pm, Bruno, ΙΣ2, MSc thesis project presentation and PhD project workplan
June 9, 4pm, Panos, Coarse-Grained simulations: Parameterization and self-assembly of lipid bilayers
June 30, 4pm, Michalis, Modeling the glycosylated state of the spike protein variants on a model cell membrane
July 5, 4pm, Danai, Modeling the active state of PI3Ka
Summer Break
September 16, 2pm, Jon, "Proton mediated enzyme communication and catalysis".
September 20, 3pm, Melina, "Ανάλυση κοιλοτήτων πρόσδεσης της ογκοπρωτεΐνης KRAS-4B με Μοριακές Δυναμικές προσομοιώσεις"
September 30, 3pm, Eleftheria, "Μοριακές Δυναμικές προσομοιώσεις του διμερισμού της ογκοπρωτεΐνης KRAS-4B"
October 7, 3pm, Group gathering, start of the semester
October 14, 3pm, Zoi, IS2, "Theoretical Study of Cyanotoxin Degradation: Background and Preliminary studies"
October 21, 2pm, Panagiotis Koukos, Utrecht University, "Perspectives on biomolecular simulation: From MD to Docking"
November 15, 2pm, Alexis, "Investigating allosteric networks in proteins using computational methods"
November 18-19, 3-8pm, "Online Conference of the European Chemical Society, Theoretical and Computational Division"
December 1, 3 pm, Panos "Shape-restrained modelling of protein-small molecule complexes with HADDOCK."
December 3, 10.30 am, Sofia, "Adaptive Sampling Simulations and Markov State Modeling"
December 13, 10.30 am, Danai, "Understanding how kinase domain mutations of PI3Kα alter lipid kinase activity using Molecular Dynamics simulations"
December 17, 12 pm, Michalis
Christmas Break
January 18, 3 pm, Danai, zoom meeting, "Allostery in Membrane Proteins"
January 26, 3 pm, Isidora, zoom meeting, Investigation of BMAA and its carbamate adducts as potential inhibitors of
the glutamate receptor AMPA using MD/FEP calculations
February 3, 4 pm, Danai, zoom, "Allostery in Membrane Proteins"
February 15, 2-5pm, ΙΣ2, Final presentations by students of "Molecular Modeling of Biomolecules" 2021-2022 Class.
February 17, 5 pm, Danai, zoom, "Investigating the protein-membrane interface"
February 23, 2.30 pm, Danai "Investigating the protein-membrane interface"
February 24, 6pm, 10th EFMC-YSN MedChemBioOnline: What Can the Medicinal Chemists Learn from Data Sciences?
March 3, 6.15pm, online, Prof. Xavier Barril, "Robustness of protein-ligand complexes: Applications in structure-based virtual screening", The online stream will be provided here.
March 10, 4 pm, Alexis PhD thesis mock exam
Easter Break
May 4, 16:05AM - 16:35 "Rapid Discovery of Potent Inhibitors of the Main Protease of SARS-CoV2", William Jorgensen (Yale University)Register here: https://t.co/w0RCjjraQ4
May 5, 5-6.30pm,
"Everything You Wanted to Know About Alchemical Free Energy Calculations But Were Afraid to Ask"Antonia Mey, University of Edinburgh
"Applications and Impact of Binding Free Energy Calculations in Drug Discovery"
Christina Schindler, Merck Healthcare KGaA
Register here: https://zoom.us/meeting/register/tJAvce-hqzIoH9DFjvlpKKmHbhNMTXtUkcWi
May 12, 4pm, Valery Lutsyk, "Extending the MARTINI 3 Coarse-Grained Force Field to Carbohydrates".
May 30, 3pm, Klea, ΙΣ2, Investigating the structure and dynamics of Myc inhibitors of the oncoprotein Myc
May 26, 4pm, Celia ΙΣ2, "Free Energy Perturbation calculations to study neurotoxic binding on the AMPA receptor".
June 2, 4pm, Bruno, ΙΣ2, MSc thesis project presentation and PhD project workplan
June 9, 4pm, Panos, Coarse-Grained simulations: Parameterization and self-assembly of lipid bilayers
June 30, 4pm, Michalis, Modeling the glycosylated state of the spike protein variants on a model cell membrane
July 5, 4pm, Danai, Modeling the active state of PI3Ka
Summer Break
Academic Year 2020-2021
September 25, 5 pm, Zoom, Katerina Barbidi and Katerina Basdeki, Presentation of internship projects
October 2, 3 pm, Zoom, Zoi Diamanti, "Στατιστική Μηχανική Μελέτη της Νευροτοξίνης β-Ν-Μεθυλάμινο-L-αλανίνη (BMAA) και Καρβαμιδικών Ενώσεων της σε Υδατικό Διάλυμα με την Μέθοδο Μοριακής Δυναμικής Προσομοίωσης"
October 19, 10 am, teleconference room, Ioannis Andreadelis, "Studying the dimerization of KRas-4B on the plasma membrane using molecular simulations"
November 5, 3 pm, zoom meeting, Alexis Chatzigoulas, "Prediction of protein membrane binding interfaces using machine learning"
November 11-13, Free Energy meeting, 6.30 - 9.30pm, please register
November 19, 3 pm, zoom meeting, Michalis Papadourakis, PhD Thesis presentation, "Molecular Dynamics based methods for calculating binding free energies and selectivity of pharmaceutical target inhibitors"
November 27, 3 pm, zoom meeting, Isidora Diakogiannaki, "BMAA and its carbamate adducts as potential inhibitors of glutamate receptors."
December 16, 6pm, zoom meeting (please register): "Molecular Simulations in the Time of COVID19 and Beyond,
Prof. Rommie Amaro
December 17, 3 pm, Prof. Michael Levitt: "50 years of force field for Bio-Design: From empirical to knowledge-based, to quantum mechanical to machine learning". 1st International BioDesign conference.
Christmas Break
January 14, 3 pm, zoom meeting, Sofia Kiriakidi, PhD mock exam, «Applications of theoretical and biophysical studies on rational drug design»
January 26, 2.30pm, zoom meeting, Final Exam of Computer Modeling of Biomolecules
February 4, 11.30am, Dr. Richard Henchman (University of Manchester), "Entropy and analysis of molecular simulations". Register here: https://www.ccpbiosim.ac.uk/entropy2021. Recording available here.
February 11, 3pm, zoom meeting, Zoi Diamanti, Theoretical study of cyanotoxin degradation for the purification of water resources
February 15-19, 7th Virtual Winter School for Computational Chemistry, register here: https://winterschool.cc/
February 25, 2pm, Alexis, "Predicting protein dynamics from evolutionarily conserved pathways using Graph Neural Networks"
March 4, 2pm, Eleni Chousa, "Part 1: Transport properties of polymeric systems based on poly (ethylene glycol)" and "Part 2: Dynamics of dense suspensions of mechanosensitive microorganisms".
March 11, 3 pm, Dr. Eleni Michael, University of Cyprus, "High-Throughput Computational Protein Design: Development and Applications".
March 18, 3pm, Isidora, "Studying the stability of glutamate, BMAA and its adducts on the glutamate receptor AMPA using MD simulations."
March 22, 10pm (Athens), Professor Peter Tieleman, University of Calgary (Canada): "Insights In Lipid-Protein Interactions from Computer Simulations".
Zoom link here.
March 24, 11:00-11.45am (Athens time) Dr. Elisa Fadda "Functional role of the glycan shield in the activation of the SARS-CoV-2 S protein" , EuroHPC Summit Week 2021, register here.
March 29-31, 4th Conference on Multiscale Modelling of Condensed Phase and Biological Systems - CCPBioSim & CCP5, Register here.
April 1, 3pm, Danae Kotzampasi, University of Crete, Computational studies for protein function and for the discovery of novel potent protein modulators
April 8, 3pm, Melina, "An overview of binding pocket analysis of the oncoprotein KRAS-4B in model cell membranes and perspectives on time-dependent binding pocket analysis studied with MD simulations"
April 15, 3pm, Eleftheria, "A literature review on Coarse-grained MD simulations to study the dimerization of the oncoprotein KRAS-4B in model cell membranes: "
April 22-24, Workshop on Computer Simulations and Theory of Macromolecules. Register here.
Easter break
May 13, 3pm, zoom meeting, Zoi Diamanti, "Literature review on the theoretical study of cyanotoxin degradation for the purification of water resources"
May 20, 2pm, zoom meeting, Themis Aivaliotis, "Investigating the structure and dynamics of Myc inhibitors bound on the intrinsically disordered oncoprotein Myc"
May 27, 6pm, Δρ. Ευαγγελία Χρυσίνα, «Ξετυλίγοντας το νήμα της πρωτεϊνικής δομής»
June 10, 6pm, Kαθ. Θωμάς Μαυρομούστακος, “Χρήσιμες Γλωσσικές Επισημάνσεις κατά τη Συγγραφή Μεταπτυχιακών και
Διδακτορικών Εργασιών»
June 15-17, 6pm-9pm, Workshop on Free Energy Methods in Drug Design, Register here
June 22, 6pm, zoom meeting, Isidora's mock exam, "Στατιστική Μηχανική Μελέτη μέσω Μοριακής Δυναμικής Προσομοίωσης της δράσης της β Ν μεθυλάμινο L αλανίνης και των καρβαμιδικών παραγώγων της ως αναστολείς του γλουταμινικού υποδοχέα ΑΜΡΑ."
June 24, 10.30am, Themis' mock exam, "Αξιολόγηση πιθανών αναστολέων του ογκογονιδίου c-Myc με προσομοιώσεις Μοριακής Δυναμικής"
June 25, Isidora's exam, "Στατιστική Μηχανική Μελέτη μέσω Μοριακής Δυναμικής Προσομοίωσης της δράσης της β Ν μεθυλάμινο L αλανίνης και των καρβαμιδικών παραγώγων της ως αναστολείς του γλουταμινικού υποδοχέα ΑΜΡΑ."
June 28, 10am, Themis diploma thesis exam, "Αξιολόγηση πιθανών αναστολέων του ογκογονιδίου c-Myc με προσομοιώσεις Μοριακής Δυναμικής"
July 1, 11am, Kαθ. Θωμάς Μαυρομούστακος, Τμήμα Χημείας, "Χρήσιμες Γλωσσικές Επισημάνσεις κατά τη Συγγραφή Μεταπτυχιακών και Διδακτορικών Εργασιών»
Summer Break - end of the academic year
Academic Year 2019-2020
September 10, 10am IS2, Dora, "Investigating the structure and dynamics of the intrinsically disordered oncoprotein Myc"
September 26, 3pm BRFAA Amphitheater, Stefan, GSPD Seminar, "Ιnvestigating the dynamics and dimerization of oncoprotein KRas-4B through molecular simulations."
October 1, 10am IS2, Dimitris, mock exam, "Using Free Energy Perturbation calculations as a predictive tool in lead optimization"
October 15, 10am IS2, Christos, "Simulating the protein dimerization process using coarse-grained MD simulations"
October 29, 12pm IS2, Themis Lazaridis, "Computational Studies of Protein-Membrane interactions"
November 1, 10am IS2, Alexis, "Prediction of protein membrane binding interfaces using machine learning"
November 11, 11am IS2, Christophe Chipot, "Taming rugged free energy landscapes using an average force"
November 19, 10am IS2, Anastasia, "Studying the structure and dynamics of the oncoprotein KRas-4B on the plasma membrane using molecular simulations".
December 3, 12pm IS2, Katerina, "Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3"
Christmas Break
January 21, 10am IS1, Dimitra Panou (Department of Informatics, UoA), DeepFoldit - A Deep Reinforcement Learning Neural Network Folding Proteins
January 23, 10am IS2, Ioannis Andreadelis (Department of Chemistry, UoA), NMR spectroscopy and molecular dynamics simulations for the study of cyclodextrin complexes with bioactive compounds.
January 28, 10am IS2, Katerina, "Free energy perturbation calculations as a Lead Optimization Method: The case of Arp2/3"
January 29, Final Exam of Computer Modeling of Biomolecules, 10am - 1pm, teleconference room
February 3, Human Brain Project Open Day
February 6, GSPD Seminar, 2.15pm, BRFAA Amphitheater, Anastasia, "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"
February 6, 3.30-6.30pm BRFAA Amphitheater, HBP CDP6 Mini Symposium: "Computational Drug Design",
February 11, 10am IS2 Shafi Khan, "Sequential ligand and structure-based virtual screening approach for the identification of potential G protein-coupled estrogen receptor-1 (GPER-1) modulators"
February 20, 10am IS2 Christos"Simulating the protein dimerization process using coarse-grained MD simulations"
February 25, 3pm IS2, Anastasia, "Studying the structure and dynamics of the oncoprotein KRas-4B on the plasma membrane using molecular simulations".
March 10-11, GRNET course on Machine Learning in HPC
March 17, 10am IS2, Giannis Nastos, "Creating functionalized nanoparticles for simulation"
March 31, 10am IS2, Alexis, "Prediction of protein membrane binding interfaces using machine learning"
April 7, 10am IS2, Ioannis, "KRAS signaling in health and disease. Opportunities for drug discovery"
Easter Break
June 4, 4pm IS2, Giannis Nastos, mock exam, "A web-based tool for the creation of functionalized nanoparticles"
June 25, 4pm IS2, Sofia Kiriakidi, "Exploring the role of the lipid bilayer in the structure and function of membrane proteins and associated drugs"
July 9, 4pm IS2, Giannis Vaxevanakis, W-DIAMOnD: Finding gene pathways associated with diseases and implementation to protein allosteric pathways.
July 27, 4pm, IS2, Christos Lamprakis, "Evaluating Coarse-Grained Molecular Dynamics simulations for studying protein dimerization in aqueous and membrane environments"
Academic Year 2018 - 2019
October 12, IS2, 6pm - mock exam Cleopatra: Developing a real time gene database for an Android application
October 19, 9.15am ΙΣ2 - MSc thesis Exam, Cleopatra: Developing a real time gene database for an Android application
October 25, 1-3pm, ΙΣ1 - Elena: Free Energy Perturbation (FEP) / MD calculations applied to lead optimization: The case of Arp2/3
November 12 - Chris Chipot, 12pm, amphitheater: "The Dangerous Liaisons between Detergents and Membrane Proteins" and "Frontiers in free-energy calculations of biological systems"
November 20 - Alexis, 4-6pm, ΙΣ1: Investigating Allostery in Enzymes using Computational Methods
December 7 - Dora, 6.30pm, ΙΣ1: Computational Study of the Tacticity Effect on the Conformational Properties of Polypropylene and Poly(ethylene-propylene) Copolymers
December 10, Leandro, 5pm, ΙΣ1: Design, synthesis and biological evaluation of antivirals against chikungunya virus
December 18, Anastasia 4-6pm, ΙΣ1 (IL33)
Christmas break
February 18, Dora 5-7pm, ΙΣ2 - Structure and dynamics of the oncoprotein Myc and development of novel anti-Myc inhibitors
January 29, Michalis, 6.15-8pm, ΙΣ1 - (TBA)
February 4-5, PRACE Workshop, GRNET
February 6, Leandro, 530pm IS2, Lead optimization of antivirals against chikungunya virus
February 12, Empowering Women in Chemistry: A Global Networking Event, University of Athens, University of Peiraus, check the programme in the links here. 9am - 4pm
February 20, Final Exam of Computer Modeling of Biomolecules, 9am - 2pm, teleconference room
February 26, Dimitris, 10am IS2, Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3.
February 27, repeat exam of Computer Modeling of Biomolecules, 1030am - 1130am, teleconference room
February 27, Dimitris Skaltsas, lecture hall of the Department of Informatics and Telecommunications, 14:00. Leveraging big data and AI to assess probability of success in drug development"
March 8, Michalis Tsakos, 1-3pm IS2, Cellular target identification and mode-of-action studies of bioactive secondary metabolites
March 19, Dimitris, 10am IS2, Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3.
March 22, Alexis, 10am IS2, Drugging peripheral membrane proteins at the protein-membrane interface
March 26, Anastasia, 10am IS2 Investigating the structure and dynamics of IL-33 as an anti-inflammatory target using MD simulations
April 9, Georgia, 10am IS2, "Biology of RXRα and the effects of the S427F mutation"
April 16, Dora, 10am, IS2 "Investigating the structure and dynamics of the oncoprotein Myc and discovery of novel Myc inhibitors"
April 22, 10 am, Stefan Doerr, IS2, "Applications of machine learning in molecular simulations"
April 23, 11am, NTUA, School of Chemical Engineering, Dimitris: "Relative Binding Free Energy Calculations as a tool in lead optimization for drug design."
April 23, 12pm, Anastasia: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"
Easter Break
June 7, 2pm, IS1, Konstantinos Vogiatzis, University of Tennessee, "Combining Machine Learning with Quantum Chemistry for Chemical Applications"
June 12, Christos, 12 pm, IS2: "Unraveling the protein-lipid interplay. Challenges towards accurate coarse grained force field system description"
June 24, Anastasia, 4 pm, NTUA Chem Eng department, mock exam: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"
June 28, Anastasia, 12.45 pm, NTUA Chem Eng department, Room32, FINAL EXAM: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"
June 28, Georgia, 3.30 pm, Γ2 mock exam: Investigation of the S427F mutation effects on the RXRα structure and dynamics
July 2, Georgia, 10 am, IS2 EXAM: Investigation of the S427F mutation effects on the RXRα structure and dynamics
July 3, 9am - 3pm, Symposium on "Computational Methods in drug design", BRFAA amphiteater
July 23, Presentation by iGEM Team 2018, 3 pm, IS1 "Toehold Switch Enabled Viral Detection via Routine Glucose Monitoring Technology."
August 2, Polydeukis Diamantis, EPFL, IS1, 2pm, "From Redox Chemistry to Conformational Dynamics: Theoretical Investigation of Chemical and Biological Systems".
August 28 - Rebecca Lait, 10am, IS1, "Using HPC to investigate the structure and dynamics of a KRAS oncogenic mutant"
August 28 - Antonio Miranda, 11am, IS1, "HPC application for candidate drug optimization using free energy perturbation calculations"
Academic Year 2017 - 2018
September 20: Γ1 2pm, Maria: Comparison of Glide and Autodock for Pose Prediction and Glide and Autodock Vina for Virtual Screening
September 28, IΣ2, 1pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
October 3, IΣ2, 3pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
October 24: IΣ2, 3pm, Anna Kapela - Design and Synthesis of Targeted Inhibitors of PI3Kα as Candidate anti- Cancer Drugs
November 20: Γ1 (1pm): Thomas Heinemann - Systematic coarse-graining procedures for molecular systems
December 11 (11:00, ΙΣ1): Matina - An automated workflow for performing free energy perturbation calculations for lead optimization
December 21 (12:30, Γ2): Alexandros - Free energy perturbation calculations for lead optimization: Comparison between FEP+ and FEP/NAMD
Christmas break
January 15 - Cleopatra - Developing databases for biological applications in Android
January 30 - Alexis, TBA - Thesis Mock Exam
February 1, Alexis, 1pm - Thesis Exam "A web-based crystallographic tool for the construction of nanoparticles"
March 1 - 10:30am-1:00pm (Γ1): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
March 5 - Aggeliki Ntorla (ΙΣ1) 11 am- "Functional characterization of missense mutations in the gene Acetyl-CoA carboxylase beta (ACC2/ACACB) found in a familial case of obesity"
March 12, Manolis Christoforou (ΙΣ1) 10am - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
March 23 - Phaeton Brotzakis (IS2) , 17.30 - Fast and accurate calculation of the affinity and binding mechanism of Benzamidine in Trypsin using VAC-MetaDynamics"
Easter Break
May 7 - Christina, 2pm, IΣ1 - Insights into the mechanism of the PI3Kα E545K activating mutation using unbiased and enhanced sampling MD simulations
May 22 - Alexandros, 1pm, ΙΣ1 - Free energy perturbation calculations for lead optimization: Comparison between FEP+, FEP/NAMD, and FEP/GROMACS on Arp2/3 complex inhibitors
May 29 - Manolis Christoforou, 10am, IΣ1, thesis mock exam - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
June 1 - Manolis Christoforou, 9am, thesis exam, Department of Informatics - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
June 8 - Cleopatra, 2pm, IΣ2 - Developing databases for biological applications in Android
June 15 - Matina, 10am, ΙΣ1 - An automated workflow for performing free energy perturbation calculations for lead optimization
June 30 - Matina, 3pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization
July 9 - Matina, 1pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization
July 11 - Matina, 10am, IS2 - EXAM - An automated workflow for performing free energy perturbation calculations for lead optimization
July 20 - Irene, 3pm, IS2, Design and development of anti-Myc inhibitors
August 3 - Petteri Vainikka, 1pm, IS2, Introduction in High throughput Virtual Screening to discover novel drug candidates
August 3 - Pedro Santos, 2pm, IS2, Introduction into Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations
August 28 - Petteri Vainikka, 10am, IS2, Final Report on High throughput Virtual Screening to discover novel drug candidates
August 28 - Pedro Santos, 11am, IS2, Final Report on Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations
August 31 - George, An automated workflow for performing free energy perturbation calculations for lead optimization
End of the Academic Year 2017-2018
September 28, IΣ2, 1pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
October 3, IΣ2, 3pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
October 24: IΣ2, 3pm, Anna Kapela - Design and Synthesis of Targeted Inhibitors of PI3Kα as Candidate anti- Cancer Drugs
November 20: Γ1 (1pm): Thomas Heinemann - Systematic coarse-graining procedures for molecular systems
December 11 (11:00, ΙΣ1): Matina - An automated workflow for performing free energy perturbation calculations for lead optimization
December 21 (12:30, Γ2): Alexandros - Free energy perturbation calculations for lead optimization: Comparison between FEP+ and FEP/NAMD
Christmas break
January 15 - Cleopatra - Developing databases for biological applications in Android
January 30 - Alexis, TBA - Thesis Mock Exam
February 1, Alexis, 1pm - Thesis Exam "A web-based crystallographic tool for the construction of nanoparticles"
March 1 - 10:30am-1:00pm (Γ1): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
March 5 - Aggeliki Ntorla (ΙΣ1) 11 am- "Functional characterization of missense mutations in the gene Acetyl-CoA carboxylase beta (ACC2/ACACB) found in a familial case of obesity"
March 12, Manolis Christoforou (ΙΣ1) 10am - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
March 23 - Phaeton Brotzakis (IS2) , 17.30 - Fast and accurate calculation of the affinity and binding mechanism of Benzamidine in Trypsin using VAC-MetaDynamics"
Easter Break
May 7 - Christina, 2pm, IΣ1 - Insights into the mechanism of the PI3Kα E545K activating mutation using unbiased and enhanced sampling MD simulations
May 22 - Alexandros, 1pm, ΙΣ1 - Free energy perturbation calculations for lead optimization: Comparison between FEP+, FEP/NAMD, and FEP/GROMACS on Arp2/3 complex inhibitors
May 29 - Manolis Christoforou, 10am, IΣ1, thesis mock exam - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
June 1 - Manolis Christoforou, 9am, thesis exam, Department of Informatics - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling
June 8 - Cleopatra, 2pm, IΣ2 - Developing databases for biological applications in Android
June 15 - Matina, 10am, ΙΣ1 - An automated workflow for performing free energy perturbation calculations for lead optimization
June 30 - Matina, 3pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization
July 9 - Matina, 1pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization
July 11 - Matina, 10am, IS2 - EXAM - An automated workflow for performing free energy perturbation calculations for lead optimization
July 20 - Irene, 3pm, IS2, Design and development of anti-Myc inhibitors
August 3 - Petteri Vainikka, 1pm, IS2, Introduction in High throughput Virtual Screening to discover novel drug candidates
August 3 - Pedro Santos, 2pm, IS2, Introduction into Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations
August 28 - Petteri Vainikka, 10am, IS2, Final Report on High throughput Virtual Screening to discover novel drug candidates
August 28 - Pedro Santos, 11am, IS2, Final Report on Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations
August 31 - George, An automated workflow for performing free energy perturbation calculations for lead optimization
End of the Academic Year 2017-2018
Academic Year 2016 - 2017
Seminars take place in the ground floor seminar room, Wednesdays 15:00 - 17:00
September 26: Zoe (SLURM conference - Technopolis Gkazi) Computer-aided drug design for novel anti-cancer agents
October 6 (Thursday, 4pm, IS2) - Youli: "Validating the Free Energy Perturbation and Replica Exchange with Solute Tempering method for lead optimization"
October 7 -9: Joint International Conference of the Hellenic Crystallographic Association & the Hellenic Society for Computational Biology and Bioinformatics
October 31 - Christina: "Optimization of Arp2/3 complex inhibitors using Free Energy Perturbation (FEP) calculations and organic synthesis & the D3R challenge"
November 22 - Anaxagoras (seminar room Γ2): "Development of data mining tools for identifying structural determinats that dictate protein-ligand interactions"
December 1 - Sofia & Christina: "The D3R challenge: the case of FXR"
December 15 (11:00 Γ1)- Giannis: "Metal-Organic Frameworks as drug delivery systems: The case of IRMOF-74-III and gemcitabine studied by a multiscale simulations"
December 19 (12.30 Γ1) - Konstantina: "Development of a crystal morphology tool & application to modeling of nanoparticles as drug delivery systems"
December 20 (12:30 IΣ2) - Konstantina: Master's thesis exam.
Christmas break
Seminars take place in the ground floor seminar room, Wednesdays 15:00 - 17:00
January 11 - Phaedon Brotzakis: Elucidating the mechanism and role of solvent for beta-lactoglobulin dimerization by using transition path sampling
January 25 - Journal Club
February 10 (13:00 ΙΣ2)- Journal Club
February 17 (13:00 ΙΣ2) - Christina - Diploma thesis mock exam: "Υπολογιστικός σχεδιασμός και σύνθεση αναστολέων του πρωτεϊνικού συμπλέγματος Arp2/3"
February 20 (17:30 Γ1) - Christina - Repeat Diploma thesis mock exam: "Υπολογιστικός σχεδιασμός και σύνθεση αναστολέων του πρωτεϊνικού συμπλέγματος Arp2/3"
February 22 - 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
February 24 - (14:30 Department of Chemical Engineering, NTUA) - Christina: Thesis Exam
March 8 (15:30 - 17:00) - Dora - Introduction into the theory of Free Energy Perturbation calculations and recent methodological advances. Structure-activity relationships of the CK666 inhibitor of the Arp2/3 complex.
Seminars take place in the ground floor seminar room, Tuesdays 13:30 - 15:30
March 17 - Michalis & Lefteris: "Introduction in Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
March 24 (13:00 - 15:00) - Giannis Tyraksis - Optimization of Arp2/3 complex inhibitor CK-869 using Free Energy Perturbation (FEP) calculations.
March 27 - D3R Challenge webinar (7pm-10 pm, teleconference room): Free Energy Perturbation calculations to predict relative binding affinities for FXR ligands
March 29 - April 2: Athens Science Festival
Easter Break
April 21 - Sophia Hirakis, UCSD, USA: Computational microscopy: insights into cardiac function at multiple scales using computational biophysics
May 2 - Panos Kakoulidis, Pasteur Institute: "Development of a pipeline for secondary and tertiary structural analysis of human miRNA targeting"
May 16 - Vasilis Georgilas, Chem Eng Dept, NTUA - "Molecular Simulation of Cavitation in Polymer networks"
May 30 - Christina: "Computer-aided drug design for binding pose and affinity predictions in the D3R Challenge 2"
June 9 (16:00) - Michalis & Lefteris: "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"
June 19 (3pm, IΣ2)- Alexis: "A web based crystallographic tool for the construction of nanoparticles"
July 4 - (3pm, ΙΣ2) Journal Club
July 11 - (3pm, ΙΣ2) Giannis Tyraskis - Optimization of Arp2/3 complex inhibitor CK-869 using Free Energy Perturbation (FEP) calculations
July 21 - (12.30pm, ΙΣ2) Nephele Agrafiotis - How to estimate convergence in Molecular Dynamics trajectories
Summer Break
Academic Year 2015 - 2016
Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00
September 28 - Giannis: Μελέτη της μοριακής βάσης του τρόπου δράσης του ανταγωνιστή του ΑΤ1 υποδοχέα, λοζαρτάνη και του μεταβολίτη του ΕΧΡ3174 με τη χρήση προσομοιώσεων Μοριακής Δυναμικής
October 9 - 11: 10th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB15)
October 26 - Dora: Optimization of Arp2/3 inhibitors using FEP calculations, synthesis, and in vitro assays
November 23 - Ioanna: Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
November 30 - Hari: Interactions of Angiotensin II with water and water/ethanol mixtures studied with MD simulations and Markov state models
December 7 - Evi: Self-assembly of anionic nanoparticles in fluid membranes using MD simulations
December 22 - Arp2/3 Greece-Turkey closing project meeting
Christmas break
January 25 - Konstantina: Modeling and simulations of functionalized magnetic nanoparticles as drug delivery systems
February 10 (Wednesday) - 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
February 22 - Ioanna: Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
March 1 - Ioanna (Tuesday, 11.00am): "Ανάλυση λιποσωμικών μεμβρανών μέσω βιοφυσικών τεχνικών (AFM και DLS) και προσομοιώσεων Μοριακής Δυναμικής". Master's thesis presentation, Αίθουσα 027 Συνεδριάσεων στο ισόγειο του κτήριου φυσικής της Σ.Ε.Μ.Φ.Ε. στο Εθνικό Μετσόβιο Πολυτεχνείο.
March 7 - Giannis: "Investigating the effect of RXRa S427F mutant on RAR-RXRa heterodimers and RXRa homotetramers"
March 28 - Christina: "Optimization of Arp2/3 complex inhibitors using Free Energy Perturbation (FEP) calculations and chemical synthesis"
April 5 - Marianna Kotzabasaki (Univ of Crete), Tuesday 12pm - 2pm (Γ2 room): "Metal-Organic Frameworks as Efficient Materials for Drug Delivery"
Easter Break
June 13 (3-5 pm, IS2) - Journal club
June 23 (3-5 pm, amphitheater) - Zoe: "Developing allosteric modulators for PIK3CA oncogenic mutants"
June 27 (3-5 pm IS2)- Journal club
July 11 (3-5 pm Γ1) - Marilena: Discovery of Novel Myc Inhibitors guided by Structure- and Ligand-based Screening
July 29 (3 pm, room Γ2) - Juan Eiros Zamora: "Troponin structure: its modulation by Ca2+ and phosphorylation studied by Molecular Dynamics simulations"
August 2 (1pm) - Sophia Hirakis (University of California, San Diego): "Stochastic Sub-cellular Investigations of Calcium Induced Calcium Release in Cardiomyocytes"
August 29 (1.00pm) - Samantha: Molecular Dynamics Simulations of the human Thymidine Kinase 1 enzyme
August 29 (1.30pm) Juan: Reranking Docking Results in ChemBioServer
October 9 - 11: 10th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB15)
October 26 - Dora: Optimization of Arp2/3 inhibitors using FEP calculations, synthesis, and in vitro assays
November 23 - Ioanna: Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
November 30 - Hari: Interactions of Angiotensin II with water and water/ethanol mixtures studied with MD simulations and Markov state models
December 7 - Evi: Self-assembly of anionic nanoparticles in fluid membranes using MD simulations
December 22 - Arp2/3 Greece-Turkey closing project meeting
Christmas break
January 25 - Konstantina: Modeling and simulations of functionalized magnetic nanoparticles as drug delivery systems
February 10 (Wednesday) - 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
February 22 - Ioanna: Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
March 1 - Ioanna (Tuesday, 11.00am): "Ανάλυση λιποσωμικών μεμβρανών μέσω βιοφυσικών τεχνικών (AFM και DLS) και προσομοιώσεων Μοριακής Δυναμικής". Master's thesis presentation, Αίθουσα 027 Συνεδριάσεων στο ισόγειο του κτήριου φυσικής της Σ.Ε.Μ.Φ.Ε. στο Εθνικό Μετσόβιο Πολυτεχνείο.
March 7 - Giannis: "Investigating the effect of RXRa S427F mutant on RAR-RXRa heterodimers and RXRa homotetramers"
March 28 - Christina: "Optimization of Arp2/3 complex inhibitors using Free Energy Perturbation (FEP) calculations and chemical synthesis"
April 5 - Marianna Kotzabasaki (Univ of Crete), Tuesday 12pm - 2pm (Γ2 room): "Metal-Organic Frameworks as Efficient Materials for Drug Delivery"
Easter Break
June 13 (3-5 pm, IS2) - Journal club
June 23 (3-5 pm, amphitheater) - Zoe: "Developing allosteric modulators for PIK3CA oncogenic mutants"
June 27 (3-5 pm IS2)- Journal club
July 11 (3-5 pm Γ1) - Marilena: Discovery of Novel Myc Inhibitors guided by Structure- and Ligand-based Screening
July 29 (3 pm, room Γ2) - Juan Eiros Zamora: "Troponin structure: its modulation by Ca2+ and phosphorylation studied by Molecular Dynamics simulations"
August 2 (1pm) - Sophia Hirakis (University of California, San Diego): "Stochastic Sub-cellular Investigations of Calcium Induced Calcium Release in Cardiomyocytes"
August 29 (1.00pm) - Samantha: Molecular Dynamics Simulations of the human Thymidine Kinase 1 enzyme
August 29 (1.30pm) Juan: Reranking Docking Results in ChemBioServer
Academic Year 2014 - 2015
Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00
October 8 (15:00, Teleconference room) - George: Mechanistic and inhibition studies of the Arp2/3 complex, a key regulator of the actin cytoskeleton
October 10-12 : 9th Conference of the Hellenic Society for Computational Biology and Bioinformatics
October 24 (16:30) - Eva - "Interactions of Strongly and Weakly Bound Water Molecules to Protein Binding Sites and Propensity for Replacements"
November 10 - Spyros - "Simulations of Arp2/3 Complex. Part I: CA Activator, Part II: CK666 Inhibitor"
November 13-15: 1st International Conference: From Drug Discovery to Drug Delivery
December 1 - George - "Investigation of the activation mechanism of the Arp2/3 complex using standard and steered MD simulations."
December 8 (15:00 - 17:00)- Hari - "Insights into the mechanism of overactivation of E545K PI3Kalpha mutant using un-biased and steered molecular dynamics simulations."
December 18 (12:00 - 15:00 - Αιθουσα Γ1)- Marilena: Computational Resources for Drug Discovery (review of the EMBL-EBI workshop)
Christmas break
January 14, 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
January 23, 13:00 - 15:00 - Αιθουσα Γ1 -Evi - "Investigation of the molecular basis of action of the AT1 antagonist losartan and its metabolite EXP3174 using a coarse-grained and all-atom molecular dynamics simulations"
February 9 - Marilena - Design and development of anti-Myc inhibitors
March 2 - Discussion of working paper
March 17-18 - Arp2/3 Greece-Turkey meeting
See the schedule of the meeting here
Easter break
25 May (4 pm) - Prof. Erik Reimhult - Synthesis and assembly of superparamagnetic core-shell nanoparticles for drug delivery capsules
7-10 June - 9th Joint Meeting in Medicinal Chemistry, Athens, Greece
25 June (1 pm) - Prof. Nikos Tsoukias - Computational modeling of cellular function: Calcium-nitric oxide signaling and the regulation of vascular tone
The following meetings will take place in room Γ2 (a new seminar room that has opened in the opposite wing of the third floor). 10:15 am - 12:00 pm
9 July - Evi - Investigating nanoparticle cellular penetration for enhanced drug delivery
13 July (13:30pm EXCEPTIONALLY) - Marilena- Structure and ligand-based studies to discover new inhibitors of the Myc oncoprotein.
16 July - Spyros: Studies of conformational analysis of Arp2/3
20 July - Hari: Studying the mechanism of overactivation of E545K PI3Kalpha mutant
Summer Break
October 10-12 : 9th Conference of the Hellenic Society for Computational Biology and Bioinformatics
October 24 (16:30) - Eva - "Interactions of Strongly and Weakly Bound Water Molecules to Protein Binding Sites and Propensity for Replacements"
November 10 - Spyros - "Simulations of Arp2/3 Complex. Part I: CA Activator, Part II: CK666 Inhibitor"
November 13-15: 1st International Conference: From Drug Discovery to Drug Delivery
December 1 - George - "Investigation of the activation mechanism of the Arp2/3 complex using standard and steered MD simulations."
December 8 (15:00 - 17:00)- Hari - "Insights into the mechanism of overactivation of E545K PI3Kalpha mutant using un-biased and steered molecular dynamics simulations."
December 18 (12:00 - 15:00 - Αιθουσα Γ1)- Marilena: Computational Resources for Drug Discovery (review of the EMBL-EBI workshop)
Christmas break
January 14, 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
January 23, 13:00 - 15:00 - Αιθουσα Γ1 -Evi - "Investigation of the molecular basis of action of the AT1 antagonist losartan and its metabolite EXP3174 using a coarse-grained and all-atom molecular dynamics simulations"
February 9 - Marilena - Design and development of anti-Myc inhibitors
March 2 - Discussion of working paper
March 17-18 - Arp2/3 Greece-Turkey meeting
See the schedule of the meeting here
Easter break
25 May (4 pm) - Prof. Erik Reimhult - Synthesis and assembly of superparamagnetic core-shell nanoparticles for drug delivery capsules
7-10 June - 9th Joint Meeting in Medicinal Chemistry, Athens, Greece
25 June (1 pm) - Prof. Nikos Tsoukias - Computational modeling of cellular function: Calcium-nitric oxide signaling and the regulation of vascular tone
The following meetings will take place in room Γ2 (a new seminar room that has opened in the opposite wing of the third floor). 10:15 am - 12:00 pm
9 July - Evi - Investigating nanoparticle cellular penetration for enhanced drug delivery
13 July (13:30pm EXCEPTIONALLY) - Marilena- Structure and ligand-based studies to discover new inhibitors of the Myc oncoprotein.
16 July - Spyros: Studies of conformational analysis of Arp2/3
20 July - Hari: Studying the mechanism of overactivation of E545K PI3Kalpha mutant
Summer Break
Academic Year 2013 - 2014
Seminars take place in the THIRD floor seminar room, Fridays 10:15 - 12:00
October 10 - Visit in Scienomics http://scienomics.com/ (NCSR Demokritos)
October 24 - George: "The Molecular Basis of Action of the AT1 Antagonist Losartan"
November 12 (12-2pm) - Ross Walker: "Lights, Computer, Action: Accelerated Molecular Dynamics, from Enzyme Activation to Membrane Dynamics"
November 21 - Evi: "Free Energy Calculations of Aminoadamantane Blockers of Influenza A/M2TM Pore"
November 29 (1 - 3pm) - Hari: "The effect of oncogenic mutation E545K on the conformation of PI3Ka"
December 12 - George: "Progress toward inhibition and mechanistic studies of the Arp2/3 complex"
Christmas break
January 23 - Lecture in NTUA by Dr. Spyros Vicatos - "Coarse - Grained Models for biological simulations, formulation and applications"
February 14 (Friday, 13:00-15:00 exceptionally) - Spyros Vicatos - Simplified Models for the studies of proteins, applications and recent advances."
March 7th - Evi & Zoe - Discussion of working paper (Nanoparticle:membrane interactions)
March 14 - Arp2/3 Meeting, Talks by George Patargias, Zoe Cournia, Yavuz Ergun
March 28 - Evi & Zoe - Discussion of working paper (H1047R PI3Ka mechanism of over-activation)
April 14 - Marilena (12pm - 2pm - IS2) - The Myc oncoprotein as a cancer drug target: Literature review and proposed studies for drug design
Easter Break
May 9 - Harris - ΠΕΙΡΑΜΑΤΙΚΗ ΚΑΙ ΥΠΟΛΟΓΙΣΤΙΚΗ ΜΕΛΕΤΗ ΤΗΣ ΑΛΛΗΛΕΠΙΔΡΑΣΗΣ ΑΜΙΝΟΑΔΑΜΑΝΤΑΝΙΚΩΝ ΠΡΟΣΔΕΤΩΝ ΜΕ ΤΟΝ ΔΙΑΜΕΜΒΡΑΝΙΚΟ ΠΟΡΟ ΤΟΥ ΙΟΝΤΙΚΟΥ ΔΙΑΥΛΟΥ ΤΗΣ ΠΡΩΤΕΪΝΗΣ ΤΟΥ IOY ΤΗΣ INFLUENZA A/M2
May 12 - 11:30- Harris Ioannidis - Master's defense - School of Pharmacy, Room ΑΦΧ
May 16 - Evi - Research Seminar: Molecular dynamics simulations of the wild-type and H1047R mutant PI3K?: Insights to the design of mutant specific inhibitors.
May 23 - Hari - Study of the E545K PI3Ka mutation
May 27 (15:30 - 17:00 Library) - Zoe & Evi - Discussion of working paper
June 5 (16:30 - 18:00 Γ1 seminar room)- George - Research Seminar: MD simulations of the Arp2/3 complex with bound VCA and actin
June 16 - Discussion of Chapter 11 (free energy methods)
June 23 - (16:00-17:00, Library) Discussion of working paper
July 7 - (13:30 - 15:00, teleconference room) Eva - Master thesis presentation "DISCOVERY OF POTENT NURR1 ACTIVATORS USING COMPUTER-AIDED DRUG DESIGN FOR THE TREATMENT OF PARKINSON'S DISEASE"
July 11 - Eva's Master thesis presentation (Department of Chemical Engineering, U Patras)
July 18 - Hari - Study of the E545K PI3Ka mutation Part II
Summer Break
Academic Year 2012 - 2013
Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00
Sept. 25 TUESDAY at 11am exceptionally - Thomas: "Elucidating the oncogenic mechanism of the H1047R PI3Kalpha mutant kinase through molecular dynamics simulations"
Oct. 8 – Eva: “NURR1 as a target to treat Parkinson's disease: Literature Review and Proposed Studies”
Oct. 22 – George at 10:15 exceptionally: “Inhibition and mechanistic studies of the Arp2/3 complex through docking and MD simulations.”
Nov. 6 – cancelled
Nov. 20 (TUESDAY) – Evi: "The effect of cholesterol in membrane phase transitions and NP translocation"
Dec. 4 (TUESDAY at 12pm exceptionally) – Harris – "Influenza A virus (M2TM)-adamantanes Studies: Peptide synthesis, ITC measurements, and FEP calculations"
Dec. 17 – Ming Han – "An in silico study of the PI3K isoform-specific inhibition"
Christmas Break
Jan. 28 - Eva: Journal Club
Feb. 21 - (11am - 1pm) Professor D Drikakis: "Computational Science Modelling for Biomedical applications"
Feb 25 - George: Journal Club
Mar. 4 - Evi: Journal Club
Mar. 19 - Ming Journal Club
Apr. 15 - Harris: Journal Club
April 23 - George: "Progress toward inhibition and mechanistic studies of the Arp2/3 complex"
Easter break
May 27 - Ming: TBA
June 10 - Evi: Studying the Influence of Cholesterol on Nanoparticle Partitioning into Lipid Membranes".
July 8 - Eva: Master's thesis presentation
July 15 - Harris: Master's thesis presentation
Summer Break
October 24 - George: "The Molecular Basis of Action of the AT1 Antagonist Losartan"
November 12 (12-2pm) - Ross Walker: "Lights, Computer, Action: Accelerated Molecular Dynamics, from Enzyme Activation to Membrane Dynamics"
November 21 - Evi: "Free Energy Calculations of Aminoadamantane Blockers of Influenza A/M2TM Pore"
November 29 (1 - 3pm) - Hari: "The effect of oncogenic mutation E545K on the conformation of PI3Ka"
December 12 - George: "Progress toward inhibition and mechanistic studies of the Arp2/3 complex"
Christmas break
January 23 - Lecture in NTUA by Dr. Spyros Vicatos - "Coarse - Grained Models for biological simulations, formulation and applications"
February 14 (Friday, 13:00-15:00 exceptionally) - Spyros Vicatos - Simplified Models for the studies of proteins, applications and recent advances."
March 7th - Evi & Zoe - Discussion of working paper (Nanoparticle:membrane interactions)
March 14 - Arp2/3 Meeting, Talks by George Patargias, Zoe Cournia, Yavuz Ergun
March 28 - Evi & Zoe - Discussion of working paper (H1047R PI3Ka mechanism of over-activation)
April 14 - Marilena (12pm - 2pm - IS2) - The Myc oncoprotein as a cancer drug target: Literature review and proposed studies for drug design
Easter Break
May 9 - Harris - ΠΕΙΡΑΜΑΤΙΚΗ ΚΑΙ ΥΠΟΛΟΓΙΣΤΙΚΗ ΜΕΛΕΤΗ ΤΗΣ ΑΛΛΗΛΕΠΙΔΡΑΣΗΣ ΑΜΙΝΟΑΔΑΜΑΝΤΑΝΙΚΩΝ ΠΡΟΣΔΕΤΩΝ ΜΕ ΤΟΝ ΔΙΑΜΕΜΒΡΑΝΙΚΟ ΠΟΡΟ ΤΟΥ ΙΟΝΤΙΚΟΥ ΔΙΑΥΛΟΥ ΤΗΣ ΠΡΩΤΕΪΝΗΣ ΤΟΥ IOY ΤΗΣ INFLUENZA A/M2
May 12 - 11:30- Harris Ioannidis - Master's defense - School of Pharmacy, Room ΑΦΧ
May 16 - Evi - Research Seminar: Molecular dynamics simulations of the wild-type and H1047R mutant PI3K?: Insights to the design of mutant specific inhibitors.
May 23 - Hari - Study of the E545K PI3Ka mutation
May 27 (15:30 - 17:00 Library) - Zoe & Evi - Discussion of working paper
June 5 (16:30 - 18:00 Γ1 seminar room)- George - Research Seminar: MD simulations of the Arp2/3 complex with bound VCA and actin
June 16 - Discussion of Chapter 11 (free energy methods)
June 23 - (16:00-17:00, Library) Discussion of working paper
July 7 - (13:30 - 15:00, teleconference room) Eva - Master thesis presentation "DISCOVERY OF POTENT NURR1 ACTIVATORS USING COMPUTER-AIDED DRUG DESIGN FOR THE TREATMENT OF PARKINSON'S DISEASE"
July 11 - Eva's Master thesis presentation (Department of Chemical Engineering, U Patras)
July 18 - Hari - Study of the E545K PI3Ka mutation Part II
Summer Break
Academic Year 2012 - 2013
Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00
Sept. 25 TUESDAY at 11am exceptionally - Thomas: "Elucidating the oncogenic mechanism of the H1047R PI3Kalpha mutant kinase through molecular dynamics simulations"
Oct. 8 – Eva: “NURR1 as a target to treat Parkinson's disease: Literature Review and Proposed Studies”
Oct. 22 – George at 10:15 exceptionally: “Inhibition and mechanistic studies of the Arp2/3 complex through docking and MD simulations.”
Nov. 6 – cancelled
Nov. 20 (TUESDAY) – Evi: "The effect of cholesterol in membrane phase transitions and NP translocation"
Dec. 4 (TUESDAY at 12pm exceptionally) – Harris – "Influenza A virus (M2TM)-adamantanes Studies: Peptide synthesis, ITC measurements, and FEP calculations"
Dec. 17 – Ming Han – "An in silico study of the PI3K isoform-specific inhibition"
Christmas Break
Jan. 28 - Eva: Journal Club
Feb. 21 - (11am - 1pm) Professor D Drikakis: "Computational Science Modelling for Biomedical applications"
Feb 25 - George: Journal Club
Mar. 4 - Evi: Journal Club
Mar. 19 - Ming Journal Club
Apr. 15 - Harris: Journal Club
April 23 - George: "Progress toward inhibition and mechanistic studies of the Arp2/3 complex"
Easter break
May 27 - Ming: TBA
June 10 - Evi: Studying the Influence of Cholesterol on Nanoparticle Partitioning into Lipid Membranes".
July 8 - Eva: Master's thesis presentation
July 15 - Harris: Master's thesis presentation
Summer Break
Academic Year 2011-2012
Nov 7-11 – EIE Workshop
Nov 28 - George: Molecular modeling studies of viral ion channels
December 12 – Evi: “Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations.
Christmas Break
Jan. 16 – Thomas: “The c-Myc oncoprotein as a cancer drug target: molecular modeling and inhibition studies.”
Jan. 30: George – Journal Club
Feb. 13: Evi – Journal Club
March 5: Thomas – Journal Club
March 16 (11:15am): Evi – “Virtual Screening and in vitro studies targeting the mutant PI3Ka protein."
April 10: No group meeting
April 23: Harris - "Synthesis of heterocyclic compounds containing thiazole and thiazolidine ring."
May 7: George - “Inhibition studies of the Arp2/3 complex.”
May 18: George - “Inhibition studies of the Arp2/3 complex.” (Friday)
May 21: Thomas – “MD simulations of the WT and mutant PI3Ka protein: Insights into the mechanism of oncogenesis.”
June 1: Evi - Journal Club (Friday)
June 19: George - Journal Club
July 3: Thomas - Journal Club
July 17: Eva: "Molecular Dynamics Simulations of Palmitic Acid"
Summer Break
Nov 28 - George: Molecular modeling studies of viral ion channels
December 12 – Evi: “Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations.
Christmas Break
Jan. 16 – Thomas: “The c-Myc oncoprotein as a cancer drug target: molecular modeling and inhibition studies.”
Jan. 30: George – Journal Club
Feb. 13: Evi – Journal Club
March 5: Thomas – Journal Club
March 16 (11:15am): Evi – “Virtual Screening and in vitro studies targeting the mutant PI3Ka protein."
April 10: No group meeting
April 23: Harris - "Synthesis of heterocyclic compounds containing thiazole and thiazolidine ring."
May 7: George - “Inhibition studies of the Arp2/3 complex.”
May 18: George - “Inhibition studies of the Arp2/3 complex.” (Friday)
May 21: Thomas – “MD simulations of the WT and mutant PI3Ka protein: Insights into the mechanism of oncogenesis.”
June 1: Evi - Journal Club (Friday)
June 19: George - Journal Club
July 3: Thomas - Journal Club
July 17: Eva: "Molecular Dynamics Simulations of Palmitic Acid"
Summer Break
Academic Year 2010 - 2011
Dec. 2 - Zoe: "Molecular Modeling and Drug Design: An Overview"
Dec. 9 - Evi: "Insights into the mechanism of oncogenesis of the mutated PI3Kα: Literature Review and Proposed Studies"
Dec. 16 - Thomas: "Molecular Mechanics of ATP-binding cassette efflux transporters"
Dec. 20 - Dimitra: "Microscopic, dynamical and transport properties of cytochrome c oxidase studied with MD simulations: Literature Review and Proposed Studies"
Christmas break
Jan. 13, 15:00 – talk in “Optimization Techniques for Protein Docking”, Speaker: Yannis Paschalidis, EKPA - Pliroforiki
Jan. 14 - Zoe: "Force Field parameterization and Molecular Dynamics Simulations principles"
Jan. 20 – lab workshop: “Molecular Dynamics simulations and Normal Mode Analysis of BPTI in vacuum with CHARMM”. This workshop will last a full day and will introduce MD/NMA techniques, script editor “vi”, and the plotting program “xmgrace”.
Jan. 23 – talk in “Electron Microscopy basics by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 14:00
Jan. 26 (9:20 - 14:45) - Translational Workshop at IIBEAA.
Jan. 27 - NO Group Seminar - please try to attend the two structural talks and the translational workshop this week.
Jan. 28 – talk in “Single particle microscopy and electron crystallography” by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 12:00
Feb. 3 - Evi: "Molecular Dynamics simulations of peptide-membrane interactions: Insights into membrane translocation mechanisms of cell-penetrating peptides.
Feb. 10 – Feb. 24 No seminar
Mar. 3 - Thomas: "Repositioning HIV protease inhibitors to target human kinome: a chemical systems biology approach"
Mar. 10 – No seminar
Mar. 17 - Zoe: "Optimization of a NURR1/RXRalpha agonist as a means to treat Parkinson’s Disease"
Mar. 24 - Evi: "Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations"
Mar. 31 – No seminar
Apr. 7 – Giannis: “Energetic and toxicophore filtering of docking poses to improve lead identification”
Apr. 14 - Thomas: "TBA: literature review an proposed studies"
Dec. 9 - Evi: "Insights into the mechanism of oncogenesis of the mutated PI3Kα: Literature Review and Proposed Studies"
Dec. 16 - Thomas: "Molecular Mechanics of ATP-binding cassette efflux transporters"
Dec. 20 - Dimitra: "Microscopic, dynamical and transport properties of cytochrome c oxidase studied with MD simulations: Literature Review and Proposed Studies"
Christmas break
Jan. 13, 15:00 – talk in “Optimization Techniques for Protein Docking”, Speaker: Yannis Paschalidis, EKPA - Pliroforiki
Jan. 14 - Zoe: "Force Field parameterization and Molecular Dynamics Simulations principles"
Jan. 20 – lab workshop: “Molecular Dynamics simulations and Normal Mode Analysis of BPTI in vacuum with CHARMM”. This workshop will last a full day and will introduce MD/NMA techniques, script editor “vi”, and the plotting program “xmgrace”.
Jan. 23 – talk in “Electron Microscopy basics by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 14:00
Jan. 26 (9:20 - 14:45) - Translational Workshop at IIBEAA.
Jan. 27 - NO Group Seminar - please try to attend the two structural talks and the translational workshop this week.
Jan. 28 – talk in “Single particle microscopy and electron crystallography” by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 12:00
Feb. 3 - Evi: "Molecular Dynamics simulations of peptide-membrane interactions: Insights into membrane translocation mechanisms of cell-penetrating peptides.
Feb. 10 – Feb. 24 No seminar
Mar. 3 - Thomas: "Repositioning HIV protease inhibitors to target human kinome: a chemical systems biology approach"
Mar. 10 – No seminar
Mar. 17 - Zoe: "Optimization of a NURR1/RXRalpha agonist as a means to treat Parkinson’s Disease"
Mar. 24 - Evi: "Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations"
Mar. 31 – No seminar
Apr. 7 – Giannis: “Energetic and toxicophore filtering of docking poses to improve lead identification”
Apr. 14 - Thomas: "TBA: literature review an proposed studies"
