One approach to finding the conformation of minimum energy for a complicated molecule is
to perform energy minimization, perhaps coupled to more exhaustive search procedures …

We describe a method for predicting the conformations of loops in proteins and its
application to four of the complementarity determining regions [CDRs] in the …

To be of any value, a predicted model of an antibody combining site should have an
accuracy approaching that of antibody structures determined by x-ray crystallography (1.6 …

A procedure, CONGEN, for uniformly sampling the conformational spaceof short polypeptide
segments in proteins has been implemented. Because thetime required for this sampling …

Loop regions of polypeptide in homologous proteins may be classified into structural
families. A method is described by which this classification may be performed automatically …

A computer-based algorithm was used to cluster the loops forming the complementarity
determining region (CDR) 3 of the heavy chain (H3) into canonical classes. Previous …

Analyses of high resolution crystal structures have shown that antibody hypervariable loops
L1, L2, and L3 from the light chain, as well as H1 and H2 from the heavy chain, can be …

An extended simulated annealing process (ESAP) has been developed in order to obtain an
ensemble of conformations of a peptide segment from a protein fluctuating at a given …

Methods for describing a discrete number of conformational states of amino acid residues in
proteins are presented and used to investigate the topography of chain folding. The relative …

The Gō–Scheraga algorithm to produce rigid‐geometry chain closures for polypeptide
chains (N. Gō and HA Scheraga, Macromolecules, 3, 178, 1970) has been updated to allow …