Computational Approach to Site-directed Ligand Discovery.
From: Locus Pharmaceuticals, Blue Bell, Pennsylvania 19422, USA. gergely.toth@gmail.com
Proteins
- Publish Date: Aug 2007
- ISSN: 1097-0134
- Volume: 68
- Issue: 2
- Pages: 551-60
- Medium: Internet
- Language: English
- Citation (JAMA): Tóth Gergely, Mukhyala Kiran, Wells James A, et al. Computational Approach to Site-directed Ligand Discovery.. Proteins Aug 2007;68:551-60
Abstract
A computational approach, Systematic Conformational Search & Induced Fit (SCI&FI), to site-directed ligand discovery (Tethering) is presented. SCI&FI has the ability to predict the binding site, binding mode, and bound dynamics of small molecule fragments covalently tethered to a protein. The SCI&FI method was engineered with the ability to model induced fit conformational changes of the protein because of the binding of the tether. SCI&FI generates comprehensive picture of the binding preferences of the tether to the protein by elucidating potential binding sites of the tether and by describing regions of receptor space capable of conformational change because of the binding of the tether. The SCI&FI method provides a complementary approach to experimental tethering. Initial validation of the SCI&FI method is reported by predicting the 3D structure of two Interleukin-2 and an Interleukin-4 tethered-protein systems.
Mesh Headings (Keywords): Amino Acid Substitution, Binding Sites, Interleukin-2, Interleukin-4, Kinetics, Ligands, Models, Molecular, Molecular Conformation, Peptide Fragments, Protein Binding
Check for Full Text / PubMed Unique Identifier (PMID): 17444517
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