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Fold recognition by concurrent use of solvent accessibility and residue depth
Author(s) -
Liu Song,
Zhang Chi,
Liang Shide,
Zhou Yaoqi
Publication year - 2007
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.21459
Subject(s) - casp , accessible surface area , solvent exposure , protein structure prediction , computer science , artificial intelligence , pattern recognition (psychology) , residue (chemistry) , solvent , bridging (networking) , structural similarity , computational biology , protein structure , mathematics , chemistry , biology , biochemistry , computer network
Recognizing the structural similarity without significant sequence identity (called fold recognition) is the key for bridging the gap between the number of known protein sequences and the number of structures solved. Previously, we developed a fold-recognition method called SP(3) which combines sequence-derived sequence profiles, secondary-structure profiles and residue-depth dependent, structure-derived sequence profiles. The use of residue-depth-dependent profiles makes SP(3) one of the best automatic predictors in CASP 6. Because residue depth (RD) and solvent accessible surface area (solvent accessibility) are complementary in describing the exposure of a residue to solvent, we test whether or not incorporation of solvent-accessibility profiles into SP(3) could further increase the accuracy of fold recognition. The resulting method, called SP(4), was tested in SALIGN benchmark for alignment accuracy and Lindahl, LiveBench 8 and CASP7 blind prediction for fold recognition sensitivity and model-structure accuracy. For remote homologs, SP(4) is found to consistently improve over SP(3) in the accuracy of sequence alignment and predicted structural models as well as in the sensitivity of fold recognition. Our result suggests that RD and solvent accessibility can be used concurrently for improving the accuracy and sensitivity of fold recognition. The SP(4) server and its local usage package are available on http://sparks.informatics.iupui.edu/SP4.