Rapid and accurate protein side chain prediction with local backbone information

Jing Zhang, Xin Gao, Jinbo Xu*, Ming Li

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

High-accuracy protein structure modeling demands accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many known side chain prediction programs, such as SCWRL and TreePack, depend on the philosophy that global information and pairwise energy function must be used to achieve high accuracy. These programs are too slow to be used in the case when side chain packing has to be used thousands of times, such as protein structure refinement and protein design. We present an unexpected study that local backbone information can determine side chain conformations accurately. LocalPack, our side chain packing program which is based on only local information, achieves equal accuracy as SCWRL and TreePack, yet runs 4-14 times faster, hence providing a key missing piece in our efforts to high-accuracy protein structure modeling.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 12th Annual International Conference, RECOMB 2008, Proceedings
Pages285-299
Number of pages15
Volume4955 LNBI
DOIs
StatePublished - 2008
Externally publishedYes
Event"12th Annual InternationalConference on REsearch in COmputational Molecular Biology, RECOMB 2008" - Singapore, Singapore
Duration: Mar 30 2008Apr 2 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4955 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other"12th Annual InternationalConference on REsearch in COmputational Molecular Biology, RECOMB 2008"
CountrySingapore
CitySingapore
Period03/30/0804/2/08

Keywords

  • Local backbone features
  • Multiclass Support vector machines
  • Side chain prediction

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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