FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst. bioc. cam. ac. uk/fugue/), has three key features.(1) Improved environment …
Y Ye, A Godzik - Bioinformatics, 2003 - user.ceng.metu.edu.tr
Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid …
DT Jones - Journal of molecular biology, 1999 - Elsevier
A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are …
M Shatsky, R Nussinov… - … : Structure, Function, and …, 2004 - Wiley Online Library
Here, we present MultiProt, a fully automated highly efficient technique to detect multiple structural alignments of protein structures. MultiProt finds the common geometrical cores …
B John, A Sali - Nucleic acids research, 2003 - academic.oup.com
Comparative or homology protein structure modeling is severely limited by errors in the alignment of a modeled sequence with related proteins of known three‐dimensional …
Distant homologies between proteins are often discovered only after three‐dimensional structures of both proteins are solved. The sequence divergence for such proteins can be so …
J Xu, M Li, D Kim, Y Xu - Journal of bioinformatics and …, 2003 - World Scientific
This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D …
H Lu, J Skolnick - Proteins: Structure, Function, and …, 2001 - Wiley Online Library
A heavy atom distance‐dependent knowledge‐based pairwise potential has been developed. This statistical potential is first evaluated and optimized with the native structure …
In fold recognition by threading one takes the amino acid sequence of a protein and evaluates how well it fits into one of the known three-dimensional (3D) protein structures …