Methods and systems for analyzing and determining ligand-residue interaction
US7415361B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | Aug 18, 2004 |
| Grant date | Aug 19, 2008 |
| Priority date | — |
| Expiry date | Aug 27, 2024 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG16C10/00
- WIPO fieldMeasurement
- WIPO sectorInstruments
Abstract
A method implemented in the form of a computer simulation code for evaluating the free energy of binding between polypeptide amino acid residues and one or more molecular fragment types is presented. The basis of the method is a novel weighted Metropolis Monte Carlo approach for sampling the grand canonical ensemble. By making use of the properties of the grand canonical ensemble, the affinity of fragments for binding in the vicinity of each protein residue can be efficiently computed. The binding volume associated to each fragment-residue pair is estimated on the basis of a simple proximity criteria, and a useful affinity mapping of the protein surface can be obtained in this way. The analysis of such data for various fragment types provides valuable information to help identify protein binding sites, as well as to identify key fragments used for building potential drug leads.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.