An approach to loop prediction that starts with a database search is presented and
analyzed. To obtain meaningful statistics, 130 loops from 21 proteins were studied. The …

The SLoop database of supersecondary fragments, first described by Donate et al.(Protein
Sci., 1996, 5, 2600–2616), contains protein loops, classified according to structural similarity …

BLoop, a method for generating plausible loop conformations for protein models, is
described. Conformations that are compatible with the local sequence are generated by …

The structure prediction of loops with flexible stem residues is addressed in this article.
While the secondary structure of the stem residues is assumed to be known, the geometry of …

The application of all‐atom force fields (and explicit or implicit solvent models) to protein
homology‐modeling tasks such as side‐chain and loop prediction remains challenging both …

Loops are the most variable regions of protein structure and are, in general, the least
accurately predicted. Their prediction has been approached in two ways, ab initio and …

We have developed an improved sampling algorithm and energy model for protein loop
prediction, the combination of which has yielded the first methodology capable of achieving …

Abstract ArchPRED server (http://www. fiserlab. org/servers/archpred) implements a novel
fragment-search based method for predicting loop conformations. The inputs to the server …

Comparative protein structure prediction is limited mostly by the errors in alignment and loop
modeling. We describe here a new automated modeling technique that significantly …

A bank of 13,563 loops from three to eight amino acid residues long, representing motifs
between two consecutive regular secondary structures, has been derived from protein …