Blog Archives

Bio-Python

2/28/2013

Biopython is a set of freely available tools for biological computation (mainly bioinformatics calculations) written in Python by an international team of developers.

Here's a link with a good intro to the tools:
http://www.biocodershub.net/community/a-hitch-hikers-guide-to-biopython-sequences-and-alphabets/

Reading and writing common sequence (and other) file formats
Classes for the usual datatypes (sequences, alignments etc.)
Functions for the usual things you’d do with those datatypes (alignments, Blasting)
Facilities for data base queries
A very large etc., etc. There’s a lot in there.

Zoe

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Schrodinger's March 2013 webinars: Phase Shape, ensemble docking, and materials applications

2/27/2013

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Schrodinger's March 2013 seminar series begin next Tuesday, March 5. This seminar series will include presentations on Phase Shape for ligand-based shape screening and new ensemble docking practices to account for protein flexibility.

Schrodinger is also debuting a Materials Science Suite this year - Dr. Vyacheslav S. Bryantsev of Liox Power will also be presenting on computational modeling of rechargeable Li-air battery materials on March 7. Please feel free to invite your colleagues in the materials industries to join us for this materials-focused presentation!

Here is the full webinar list with dates:

Accounting for protein flexibility in virtual screening using ensemble docking

Dr. Woody Sherman
Schrödinger's Vice President, Applications Science
Abstract March 5, 2013
10 am ET Register
1pm ET Register

Computational Modeling of Rechargeable Li-Air Battery Materials
Dr. Vyacheslav S. Bryantsev
Liox Power, Senior Scientist
Abstract March 7, 2013
10 am ET Register

Using Phase Shape for rapid ligand alignment and virtual screening
Dr. Woody Sherman
Schrödinger's Vice President, Applications Science
Abstract March 12, 2013
10 am ET Register
1pm ET Register

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Current Protocols from Wiley @WileyScience

2/26/2013

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Current Protocols from the Wiley online library offer protocols in several areas such as Bioinformatics, Cell Cultures, Chemical Biology, Molecular Biology, Pharmacology and Drug Discovery and many more. They are not free, but most academic libraries should have a subscription.

Here is the list for protocols on Molecular Modeling:

Protein Structural Domains: Definition and Prediction
Iakes Ezkurdia, Michael L. Tress
Published online: November 2011
Using AutoDock for Ligand‐Receptor Docking
Garrett M. Morris, Ruth Huey, Arthur J. Olson
Published online: December 2008
Exploring Biological Networks with Cytoscape Software
Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, Gary D. Bader
Published online: September 2008
Browsing Multidimensional Molecular Networks with the Generic Network Browser (N‐Browse)
Huey‐Ling Kao, Kristin C. Gunsalus
Published online: September 2008
Using ChemBank to Probe Chemical Biology
Kathleen Petri Seiler, Heidi Kuehn, Mary Pat Happ, Dave DeCaprio, Paul A. Clemons
Published online: June 2008
Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar, Ben Webb, Marc A. Marti‐Renom, M.S. Madhusudhan, David Eramian, Min‐yi Shen, Ursula Pieper, Andrej Sali
Published online: November 2007
In Silico Drug Exploration and Discovery Using DrugBank
David S. Wishart
Published online: June 2007
Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity
Martin R. Schiller
Published online: May 2007
Comparative Protein Structure Modeling Using Modeller
Narayanan Eswar, Ben Webb, Marc A. Marti‐Renom, M.S. Madhusudhan, David Eramian, Min‐yi Shen, Ursula Pieper, Andrej Sali
Published online: October 2006
Using MSDchem to Search the PDB Ligand Dictionary
Dimitris Dimitropoulos, John Ionides, Kim Henrick
Published online: October 2006
Representing Structural Information with RasMol
David S. Goodsell
Published online: October 2005
Protein Tertiary Structure Prediction
Dong Xu, Ying Xu
Published online: May 2001
Protein Tertiary Structure Modeling
Nicolas Guex, Torsten Schwede, Manuel C. Peitsch
Published online: May 2001

Zoe

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2012 Structure-Based Drug Design Conference presentations free online

2/26/2013

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You can download complimentary speaker presentations from the CHI's 2012 Structure-Based Drug Design (SBDD) conference by simply filling in a registration form here:

Making Docking/Scoring Calculations More Accurate via Error Analysis
Authored by: Kenneth M. Merz, Jr., Ph.D., Department of Chemistry, Quantum Theory Project, University of Florida

Challenges facing computational biology
Water models and water dimer
2010 GPCR docking and modeling competition
What about the docking funnel?

Download Presentation

Rational Approaches to Improving Selectivity in Drug Design
Authored by: Woody Sherman, Ph.D., Vice President, Applications Science, Shrodinger

Factors contributing to selectivity
Shape complementarity: Clash with decoy
- Remove decoy interactions
Induced fit of target
Experimental validation

Download Presentation

Structure based Ligand Discovery for GPCRs
Authored by: Ruben Abagyan, Ph.D., Professor, Skaggs School of Pharmacy & Pharmaceutical Sciences, San Diego Supercomputer Center, University of California, San Diego

Growing understanding of GPCR structure and function
Docking to flexible sites: methods and benchmarks
2010 GPCR docking and modeling competition
Ligand guided modeling of unsolved GPCRs and alternative states

Download Presentation

Making Decisions in Fragment-Based Drug Discovery
Authored by: Rod Hubbard, Ph.D., Director, Structural Sciences, Vernalis Ltd.

Overview of fragment-based methods
- Some (old) examples of successes
Some fragmentology
- Hit rates and target druggability
- Predicting fragment poses
- Selectivity
How to make decisions on which fragments to progress?
What are the opportunities for computational methods?

Download Presentation

This is the agenda for the 2013 Structure-Based Drug Design Conference.

Zoe

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Coursera - free online courses @coursera

2/24/2013

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Here is the complete list of Coursera's free online courses in Biology & Life Sciences:

9 weeks long AIDS Emory University Feb 25th 2013
12 weeks long Introductory Human Physiology Duke UniversityMarch 2013
9 weeks long Synapses, Neurons and Brains Hebrew University of Jerusalem Mar 25th 2013
8 weeks long Medical Neuroscience Duke University April 2013
10 weeks long Computational Neuroscience University of Washington April 2013
7 weeks long Nutrition, Health, and Lifestyle: Issues and Insights Vanderbilt University Apr 19th 2013
9 weeks long Drug Discovery, Development & Commercialization University of California, San Diego Apr 22nd 2013
6 weeks long Genes and the Human Condition (From Behavior to Biotechnology) University of Maryland, College Park May 1st 2013
10 weeks long Useful Genetics The University of British Columbia May 3rd 2013
6 weeks long Canine Theriogenology for Dog Enthusiasts University of MinnesotaMay 6th 2013
6 weeks long Pensamiento Científico Universidad Nacional Autónoma de MéxicoJun 24th 2013
10 weeks long Computational Molecular Evolution Technical University of Denmark (DTU)Jul 1st 2013
6 weeks long Epigenetic Control of Gene Expression University of MelbourneJul 22nd 2013
6 weeks long Exercise Physiology: Understanding the Athlete Within University of MelbourneAug 19th 2013
6 weeks long Animal Behaviour University of MelbourneAug 26th 2013
4 weeks long Preparation for Introductory Biology: DNA to Organisms University of California, IrvineSep 2nd 2013
8 weeks long The New Nordic Diet - from Gastronomy to Health University of CopenhagenOct 15th 2013
8 weeks long Epidemics - the Dynamics of Infectious Diseases Pennsylvania State University January 2014
10 weeks long Human Evolution: Past and Future University of Wisconsin–Madison Sep 24th 2012
8 weeks long Writing in the Sciences Stanford University Jan 22nd 2013
10 weeks long Fundamentals of Human Nutrition University of Florida Jan 28th 2013
5 weeks long Critical Thinking in Global Challenges University of Edinburgh Feb 4th 2013
9 weeks long Bioelectricity: A Quantitative Approach Duke University Date to be announcedDrugs and the Brain California Institute of Technology Date to be announced
Introduction to Genetics and Evolution Duke University Date to be announced
4 weeks long Basic Behavioral Neurology University of Pennsylvania Date to be announced
6 weeks long Diabetes - a Global Challenge University of Copenhagen Date to be announced
7 weeks long Dynamical Modeling Methods for Systems Biology Icahn School of Medicine at Mount Sinai Date to be announced Experimental Genome Science University of Pennsylvania Date to be announced
Histología básica: los cuatro tejidos fundamentales Universitat Autònoma de Barcelona (Autonomous University of Barcelona) Date to be announced
5 weeks long Introduction to Systems Biology Icahn School of Medicine at Mount Sinai Date to be announced
10 weeks long Introduction to Tissue Engineering Hebrew University of Jerusalem Date to be announced
7 weeks long Network Analysis in Systems Biology Icahn School of Medicine at Mount Sinai Date to be announced
8 weeks long Origins - Formation of the Universe, Solar System, Earth and Life University of CopenhagenDate to be announced
6 weeks long Programmed cell death Ludwig-Maximilians-Universität München Date to be announced
6 weeks long The Science of Gastronomy The Hong Kong University of Science and Technology

Zoe

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Free online course on Drug Discovery, Development, and Commercialization

2/24/2013

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Coursera.org offers 323 free online courses from major universities on a variety of subjects such as: Financial Engineering and Risk Management, AIDS, Introductory Human Physiology, Synapses, Neurons and Brains and more!

The Drug Discovery, Development & Commercialization course is offered by UC San Diego (Drs Williams S. Ettouati and Joseph D. Ma). Students will learn the process of drug discovery and development through specific examples of case studies to better understand the issues facing the challenges of delivering a new drug on the market. At the completion of this course you will be able to have a better understanding of how a small or large molecule becomes a pharmaceutical drug.

The Next Session starts Apr 19th 2013 for a 9 weeks long course.

Here is the syllabus and signup form.

Zoe

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PDB Tools

2/18/2013

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Here's a collection of scripts that manipulate protein and nucleic acid pdb (structure) files.They are simple python scripts so you do not have to install or use a larger program for simple calculations.

Zoe

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Benchmark studies of NAMD and GROMACS

2/11/2013

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We have recently performed benchmark studies of different systems (ranging from 200,000 atoms to 600,000 atoms) with and without GPU acceleration for the programs NAMD and GROMACS.

Larger systems seem to benefit from GPU acceleration with GROMACS; NAMD did not scale well using the GPU version.
For systems ~200,000 atoms Gromacs scales well up to 112 cores.

See more here.

Zoe

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Funding for Travel to a Green Chemistry Meeting

2/8/2013

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Interested in green chemistry? Want to attend a conference in 2013? If you are an international student/postdoc/lecturer living in the U.S. or abroad, you can apply for the Joseph Breen Fellowship by March 1, 2013. The award covers up to $2,000 in travel expenses to qualified events. More info here.

Green chemistry in the context of the Breen Fellowship is defined as “the discovery and design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances.”

See here previous winners of the Breen Fellowship.

Zoe

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On the implementation of the AMBER force field in NAMD and GROMACS

2/5/2013

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The AMBER force field ff99SB-ILDN has been recently shown to perform best among other force fields. See paper by the Shaw group: "Systematic Validation of Protein Force Fields against Experimental Data"

However, AMBER is not free and does not scale very well on over 256 cores, which means that it is best to run the NAMD or GROMACS codes using the AMBER force field if you are running on more than 256 cores or do not have Amber.

However, you should carefully read and implement the directions in this document for use with NAMD (NOT the UIUC one), which should give you identical energies if followed carefully.

For use with GROMACS follow these instructions: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx or http://chemistry.csulb.edu/ffamber/

Zoe

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Bio-Python

Schrodinger's March 2013 webinars: Phase Shape, ensemble docking, and materials applications

Current Protocols from Wiley @WileyScience

2012 Structure-Based Drug Design Conference presentations free online

Coursera - free online courses @coursera

Free online course on Drug Discovery, Development, and Commercialization

PDB Tools

Benchmark studies of NAMD and GROMACS

Funding for Travel to a Green Chemistry Meeting

On the implementation of the AMBER force field in NAMD and GROMACS

Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

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