Introduction

Loops in proteins are flexible regions connecting regular secondary structures. They are often involved in protein functions through interacting with other molecules. The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally. Conformation sampling and energy evaluation are the two key components in loop modeling. We have developed a new method for loop conformation sampling and prediction based on a chain growth sequential Monte Carlo sampling strategy, called Distance-guided Sequential chain-Growth Monte Carlo (DISGRO). With an energy function designed specifically for loops, our method can efficiently generate high quality loop conformations with low energy that are enriched with near-native loop structures. The average minimum global backbone RMSD for 1,000 conformations of 12-residue loops is 1:53 A° , with a lowest energy RMSD of 2:99 A° , and an average ensembleRMSD of 5:23 A° . A novel geometric criterion is applied to speed up calculations. The computational cost of generating 1,000 conformations for each of the x loops in a benchmark dataset is only about 10 cpu minutes for 12-residue loops, compared to ca 180 cpu minutes using the FALCm method. Test results on benchmark datasets show that DISGRO performs comparably or better than previous successful methods, while requiring far less computing time. DISGRO is especially effective in modeling longer loops (10-17 residues).

Publications

  1. Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method.
    Cite this
    Tang K, Zhang J, Liang J, 2014-04-01 - PLoS computational biology

Credits

  1. Ke Tang
    Developer

    Department of Bioengineering, University of Illinois at Chicago, United States of America

  2. Jinfeng Zhang
    Developer

    Department of Statistics, Florida State University, United States of America

  3. Jie Liang
    Investigator

    Department of Bioengineering, University of Illinois at Chicago, United States of America

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Summary
AccessionBT006431
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJie Liang