Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex |
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Authors: | Zhang Da W Xiang Yun Gao Ai M Zhang John Z H |
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Institution: | Department of Chemistry, New York University, New York, New York 10003, USA. |
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Abstract: | We report full ab initio Hartree-Fock calculation to compute quantum mechanical interaction energies for beta-trypsin/benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire protein complex with 3238 atoms is made possible by using a recently developed MFCC (molecular fractionation with conjugate caps) approach in which the protein molecule is decomposed into amino acid-based fragments that are properly capped. The present MFCC ab initio calculation enables us to obtain an "interaction spectrum" that provides detailed quantitative information on protein-ligand binding at the amino acid levels. These detailed information on individual residue-ligand interaction gives a quantitative molecular insight into our understanding of protein-ligand binding and provides a guidance to rational design of potential inhibitors of protein targets. |
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