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Prediction of loop geometries using a generalized born model of solvation effects
Author(s) -
Rapp Chaya Sendrovic,
Friesner Richard A.
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19990501)35:2<173::aid-prot4>3.0.co;2-2
Subject(s) - solvation , implicit solvation , molecular dynamics , statistical physics , root mean square , monte carlo method , loop (graph theory) , loop modeling , homology modeling , physics , computational chemistry , protein structure prediction , biological system , chemistry , algorithm , protein structure , computer science , molecule , mathematics , quantum mechanics , biology , statistics , combinatorics , enzyme , nuclear magnetic resonance
We have carried out an extensive exploration of the possibility of predicting the structure of long loops in proteins, using an 8‐ and a 12‐residue loop in ribonuclease A as models. The native X‐ray structure is used as a template while allowing for template flexibility; this makes our work relevant to the problem of homology modeling in which the template is not precisely known. Energies are calculated with the AMBER* and AMBER94 molecular mechanics potentials and the generalized Born continuum solvation model; and conformational space is sampled by means of a combination of Monte Carlo and molecular dynamics methods. Our AMBER94 results demonstrate that we can successfully generate loops with low root‐mean‐square deviations from the native as well as excellent energetic rankings. Proteins 1999;35:173–183. © 1999 Wiley‐Liss, Inc.