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  • Title: Prediction of loop geometries using a generalized born model of solvation effects.
    Author: Rapp CS, Friesner RA.
    Journal: Proteins; 1999 May 01; 35(2):173-83. PubMed ID: 10223290.
    Abstract:
    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.
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