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CSAR - 2013 Benchmark exercise: Can you determine which protein binds a steroid?

3/27/2013

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CSAR is a community resource for Docking and Scoring Development

In their third benchmark competition, over one dozen proteins were designed to bind a steroid. Can you determine which were successful? (timeframe: 1 month and ends on 26 April 2013). See www.CSARdock.org to download the zip file.

This exercise is built around designed proteins developed by Tinberg, Khare, and Baker. This is an interesting twist on traditional docking/scoring problems because there is no existing protein data on which to train models (as was possible in the first two exercises). Three phases, with a possible fourth phase are coming up:

Phase 1: Protein design – Over one dozen proteins were designed to bind a steroid. Can you determine which were successful? (timeframe: 1 month, ending 26 April 2013)

Phase 2: Scoring – Given the set-up crystal structures of the proteins and a set of pregenerated docking decoys, can you identify the correct poses for the steroid? (timeframe: start after Phase 1 ends and run 2 weeks)

Phase 3: Selectivity – Given the set-up crystal structures of some protein-steroid complexes, can you predict the binding affinity (or relative ranking) of several steroids binding to the same protein? (timeframe: start after Phase 2 ends and run 1 month)

Phase 4: Predict the effect of protein mutations – There is extensive mutational data available. Given a subset, can you "bin" their effects into weak, moderate, significant changes in binding? (timeframe: longer and not yet determined)

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The CompBio Experiment: How far are we from an ideal Computing-as-a-Service or HPC-in-the-Cloud model? 

3/21/2013

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Cloud computing-on-demand gives end users many benefits by gaining access to additional compute resources beyond their current internal resources. But how far are we from an ideal Computing-as-a-Service or HPC-in-the-Cloud model? 

To address this question, Wolfgang Gentzsch (HPC and Cloud Projects Specialist) and Burak Yenier (VP of Operations at CashEdge) organized the Uber-Cloud Experiment to explore the end-to-end process of accessing remote resources in computer centers and in HPC Clouds, and to study and overcome the potential roadblocks. Round 1 of the experiment kicked off in July 2012. Read the results here.

Over 250 participants have already registered for Round 2 and we are still seeking computational biologists and any others who would like to be involved. To participate in Round 2 or just monitor it closely—and to receive the final Round 1 report with all findings—register at http://www.compbioexperiment.com.  

This is an open invitation to members of the Life Sciences community to join the experiment for a 3-month experiment, where they will apply the cloud computing service model to workloads on remote Cluster Computing resources in the areas of bio, pharma, and chemistry.


Our lab is a registered participant in this effort.

Zoe

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Ubuntu - the meaning

3/18/2013

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An anthropologist offered children of an African tribe a new game. He put a basket full of fruit close to a tree and told them that who would be there first would win and get all the fruits. When he gave them the start signal they all went to the tree together holding hands. They all sat down and enjoyed the delicious fruits. When the anthropologist asked why they had gone together rather than running to see who would win and reach the fruits first they said: "Ubuntu, how can one of us be happy if all the others are sad?"

Ubuntu in the Xhosa culture means: "I am, because you are, and I can only be, if you are."

Picture
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Video: Supercomputer Modelling of a Complete Human Viral Pathogen

3/13/2013

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In this video, researchers perform a reconstruction and simulation of the poliovirus using the BlueGene/Q supercomputer at the Victorian Life Sciences Computation Initiative. The poliovirus model is being used as a basis for understanding antiviral drugs, virus infection and helps us to learn how to model related viruses such as Enterovirus 71.

http://insidehpc.com/2013/03/06/video-supercomputer-modelling-of-a-complete-human-viral-pathogen/?goback=.gde_54503_member_220959831


Zoe
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In silico solubility predictions

3/12/2013

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Here is a review on solubility predictions, along with a list of the most popular softwares.
http://cadd.suda.edu.cn/Group/papers/review8.pdf

Zoe
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Visualize an trajectory created by Impact (Schrodinger)

3/11/2013

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To visualize an impact trajectory, open the panel with the Impact parameters before starting the run and click on "Record Trajectory", which is deselected by default. The option is under: Applications -> Impact -> Dynamics -> MD Parameters -> Record Trajectory".
After your trajectory is ready, you will see a "T" in your project table. Click on the "T" and a trajcetory viewing panel will open.

To prepare a video file for incorporation into PowerPoint showing your modelling results you can use the following options:
  • You can create a movie in MPEG format of the selected entries in the Project Table with Entry → Record Movie.
  • From Suite 2010 on you can create a movie in MPEG format of a sequence of Workspace views, by clicking Record Movie in the Manage Views panel.
  • You can record a movie of a Desmond (or Impact) trajectory, in the Trajectory panel.
  • You can use the Maestro Viewer ActiveX control in a PowerPoint presentation, to show a structure in a Maestro window, and manipulate it (rotate, translate, zoom) in the presentation.
See also:


http://www.schrodinger.com/kb/354

Zoe


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How can one download all PDB structure containing only helices?

3/6/2013

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Search for alpha or beta -domains/folds in the pdb using the SCOP or CATH classifications.
http://scop.mrc-lmb.cam.ac.uk/scop/

http://www.cathdb.info/


Zoe
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Computational Drug Discovery and Design volume from @SpringerPub

3/1/2013

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Riccardo Baron also put together a great computational methods volume you should have access to:http://link.springer.com/book/10.1007/978-1-61779-465-0/page/1
Here's the list of contents:

Drug Binding Site Prediction, Design, and Descriptors
A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites
  • Anthony Ivetac, J. Andrew McCammon Look Inside Get Access
Analysis of Protein Binding Sites by Computational Solvent Mapping
  • David R. Hall, Dima Kozakov, Sandor Vajda
Evolutionary Trace for Prediction and Redesign of Protein Functional Sites
  • Angela Wilkins,Serkan Erdin,Rhonald Lua,Olivier Lichtarge
Information Entropic Functions for Molecular Descriptor Profiling
  • Anne Mai Wassermann,Britta Nisius,Martin Vogt,Jürgen Bajorath

Virtual Screening of Large Compound Libraries: Including Molecular Flexibility
Expanding the Conformational Selection Paradigm in Protein-Ligand Docking
  • Guray Kuzu,Ozlem Keskin,Attila Gursoy,Ruth Nussinov Look Inside Get Access
Flexibility Analysis of Biomacromolecules with Application to Computer-Aided Drug Design
  • Simone Fulle,Holger Gohlke
On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening
  • Sara E. Nichols,Riccardo Baron,J. Andrew McCammon
Virtual Ligand Screening Against Comparative Protein Structure Models
  • Hao Fan,John J. Irwin,Andrej Sali
AMMOS Software: Method and Application
  • T. Pencheva,D. Lagorce,I. Pajeva,B. O. Villoutreix,M. A. Miteva
Rosetta Ligand Docking with Flexible XML Protocols
  • Gordon Lemmon,Jens Meiler
Normal Mode-Based Approaches in Receptor Ensemble Docking
  • Claudio N. Cavasotto
Application of Conformational Clustering in Protein–Ligand Docking
  • Giovanni Bottegoni,Walter Rocchia,Andrea Cavalli
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
  • Andrew J. Christofferson,Niu Huang

Prediction of Protein-Protein Docking and Interactions

AGGRESCAN: Method, Application, and Perspectives for Drug Design
  • Natalia S. de Groot,Virginia Castillo,Ricardo Graña-Montes,Salvador Ventura
ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking
  • Sebastian Schneider,Adrien Saladin,Sébastien Fiorucci,Chantal Prévost
Prediction of Interacting Protein Residues Using Sequence and Structure Data
  • Vedran Franke,Mile Šikić,Kristian Vlahoviček

Rescoring Docking Predictions
MM-GB/SA Rescoring of Docking Poses
  • Cristiano R. W. Guimarães
A Case Study of Scoring and Rescoring in Peptide Docking
  • Zunnan Huang, Chung F. Wong
The Solvated Interaction Energy Method for Scoring Binding Affinities
  • Traian Sulea, Enrico O. Purisima
Linear Interaction Energy: Method and Applications in Drug Design
  • Hugo Gutiérrez-de-Terán, Johan Åqvist 
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    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

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