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Prediction of loop geometries using a generalized born model of solvation effects

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.