We introduce an energy function for contact maps of proteins. In addit
ion to the standard term, that takes into account pairwise interaction
s between amino acids, our potential contains a new hydrophobic energy
term. Parameters of the energy function were obtained from a statisti
cal analysis of the contact maps of known structures. The quality of o
ur energy function was tested extensively in a variety of ways. In par
ticular, fold recognition experiments revealed that for a fixed sequen
ce the native map is identified correctly in an overwhelming majority
of the cases tested. We succeeded in identifying the structure of some
proteins that are known to pose difficulties for such tests (BPTI, sp
ectrin, and cro-protein). In addition, many known pairs of homologous
structures were correctly identified, even when the two sequences had
relatively low sequence homology, We also introduced a dynamic Monte C
arlo procedure in the space of contact maps, taking topological and po
lymeric constraints into account by restrictive dynamic rules. Various
aspects of protein dynamics, including high-temperature melting and r
efolding, were simulated. Perspectives of application of the energy fu
nction and the method for structure checking and fold prediction are d
iscussed. (C) 1996 Wiley-Liss, Inc.