January 2018 Newsletter
Our January update includes a spotlight on a new software package: EVcouplings. SBGrid.org will host a webinar with the author on Feb. 27. See below for details Are there software packages you would like to see available through BioGrids? Send a request to firstname.lastname@example.org.
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Which residues are the most evolutionarily constrained?
Calculate ECs between residues, explore these for functional relevance and map them onto known structures.
EVcouplings software is now available through BioGrids and SBGrid. It can be installed on local machines or used directly on the HMS O2 cluster. All BioGrids software is available on O2 through the BioGrids module.
SBGrid EVCouplings Webinar
Join SBGrid.org on February 27th to hear from Debora Marks's lab at Harvard Medical School about EVcouplings.
Tuesday, February 27th at 12:00pm EST
Debora Marks, Ph.D. Principal Investigator Harvard Medical School
Get complete webinar details here .
Sequence co-evolution gives 3D contacts and structures of protein complexes
Thomas A Hopf, Charlotta P I Schärfe, João P G L M Rodrigues, Anna G Green, Oliver Kohlbacher, Chris Sander, Alexandre M J J Bonvin, Debora S Marks eLife 2014;3:e03430 September 25, 2014 http://dx.doi.org/10.7554/eLife.03430
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution
Do you have a favorite software package you'd like to use in BioGrids or see highlighted here? Drop a note to email@example.com.
For a full listing of available applications see the BioGrids.org (https://biogrids.org/software/) website.
EVcouplings version 0.0.1 Protein and RNA structure, function and fitness predicted from evolutionary sequence covariation
Training sessions available to HMS trainees
Spring registrations available soon.
Feb 21 Searching with PubMed
Feb 23 Intermediate bash
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