Premium
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
Author(s) -
Skolnick Jeffrey,
Kolinski Andrzej,
Kihara Daisuke,
Betancourt Marcos,
Rotkiewicz Piotr,
Boniecki Michal
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.1172
Subject(s) - threading (protein sequence) , ab initio , protein structure prediction , cluster analysis , computer science , lattice (music) , monte carlo method , protein folding , structural bioinformatics , algorithm , protein structure , statistical physics , crystallography , artificial intelligence , chemistry , physics , mathematics , statistics , biochemistry , organic chemistry , acoustics
Abstract A combination of sequence comparison, threading, lattice, and off‐lattice Monte Carlo (MC) simulations and clustering of MC trajectories was used to predict the structure of all (but one) targets of the CASP4 experiment on protein structure prediction. Although this method is automated and is operationally the same regardless of the level of uniqueness of the query proteins, here we focus on the more difficult targets at the border of the fold recognition and new fold categories. For a few targets (T0110 is probably the best example), the ab initio method produced more accurate models than models obtained by the fold recognition techniques. For the most difficult targets from the new fold categories, substantial fragments of structures have been correctly predicted. Possible improvements of the method are briefly discussed. Proteins 2001;Suppl 5:149–156. © 2002 Wiley‐Liss, Inc.