A population-based conformational optimal algorithm using replica-exchange in ab-initio protein structure prediction

Referring to ab-initio protein structure prediction, a replica exchange based differential evolution searching method (REDE) was proposed. Firstly, employing fragment assembly technique to reduce the dimension of protein conformational space effectively, thus avoiding the entropy effect in searching. Additionally, every replica layer equipped with a conformation population, updating the population by using differential evolution algorithm, to ensure diversity of population in replicas. Moreover, it can enhance the capacity of algorithm to jump out of local minimum. The result of 10 test proteins show that the mentioned algorithm can rapidly and effectively sample from the conformational space and generated high-resolution near-native protein conformations.

[1]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[2]  David Baker,et al.  Protein Structure Prediction Using Rosetta , 2004, Numerical Computer Methods, Part D.

[3]  Yuji Sugita,et al.  Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , 2000, cond-mat/0009119.

[4]  Hongjun Bai,et al.  Assessment of template‐free modeling in CASP10 and ROLL , 2014, Proteins.

[5]  Luís C. Lamb,et al.  Three-dimensional protein structure prediction: Methods and computational strategies , 2014, Comput. Biol. Chem..

[6]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[7]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[8]  F. Ding,et al.  Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.

[9]  C. Anfinsen,et al.  The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[11]  A. Liwo,et al.  Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. , 2009, Journal of chemical theory and computation.

[12]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.

[13]  Anna Tramontano,et al.  Protein structure prediction , 2013 .

[14]  J. Bujnicki.  Protein-Structure Prediction by Recombination of Fragments , 2006 .

[15]  O. Schueler‐Furman,et al.  Progress in Modeling of Protein Structures and Interactions , 2005, Science.

[16]  D. Osguthorpe.  Ab initio protein folding. , 2000, Current opinion in structural biology.

[17]  Daniel W. Kulp,et al.  Generalized Fragment Picking in Rosetta: Design, Protocols and Applications , 2011, PloS one.

[18]  Junfeng Huang,et al.  Template-Based Protein Structure Prediction: Template-Based Protein Structure Prediction , 2011 .

[19]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[20]  Adam Zemla,et al.  Critical assessment of methods of protein structure prediction (CASP)‐round V , 2005, Proteins.

[21]  Yang Zhang,et al.  Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field , 2012, Proteins.

[22]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..