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Computational structural proteomics and virtual ligand screening

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Computational structural proteomics and virtual ligand screening

Content Provider	ACM Digital Library
Author	Abagyan, Ruben
Abstract	Large scale discovery of new human genes, gene families and isozymes creates an exciting biomedical opportunity. Advanced modeling by homology techniques can be employed to generate 3D models for most of the interesting new gene family members. This opens many new opportunities for structural structure based functional annotation and molecular design. Several key computational technologies enable structural protein modeling and rational drug design: sequence-structure relationships, multiple sequence alignments, threading molecular mechanics; global energy optimization; protein modeling by homology; structure based protein functional annotation (e.g. prediction of possible active sites, small molecule binding sites, protein-protein interaction sites, flexibility annotation); protein design and redesign using structure prediction algorithms; structural immunology, e.g. derivation and design of peptide sequence specific for a particular HLA presenting molecule based on the HLA structure; peptide-protein docking; protein-protein docking; small molecule docking and virtual ligand screening; cheminformatics algorithms and virtual chemistry.We have been developing the internal coordinate mechanics approach to structure prediction for the last 16 years. It is aimed at de novo prediction of large structural rearrangements. To achieve that goal an ICM program has been developed and combined accurate energy functions with powerful global optimization algorithm in the internal coordinate space.The most recent developments include on-the-fly calculations of accurate Poisson electrostatics using the efficient boundary element algorithm based on the analytical molecular surface. This allows to predict de novo a solution structure of a 23-residue peptide.New computational technology for virtual ligand screening allows to generate alternative receptor conformations and perform flexible docking of hundreds of thousands of virtual compounds to the binding site. The success of this technology is demonstrated on several benchmarks and in six experimental projects which tested the prediction results. For well defined binding pockets only about the initial compound set actually needs to be synthesized and tested. Using ICM docking and scoring technology we have identified new ligands in a number of cases, including cases in which a model was used instead of a crystallographic structure and a case in which protein-protein interaction has been targeted.The most interesting recent results tested experimentally include: the de novo design of novel antagonists of thyroid hormone receptor, for which no antagonists were known before and, consequently, no antagonist-bound structure was known; de novo design of ligands targeting Ephrin-Ephrin receptor interactions.
Starting Page	1
Ending Page	1
Page Count	1
File Format	PDF
ISBN	1581134983
DOI	10.1145/565196.565197
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2002-04-18
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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