This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by da Silva, R. A. Articles by Caliri, A. Search for Related Content PubMed PubMed Citation Articles by da Silva, R. A. Articles by Caliri, A.

LMProt: An Efficient Algorithm for Monte Carlo Sampling of Protein Conformational Space

Roosevelt Alves da Silva ^*, Léo Degrève ^* and Antonio Caliri 

^* Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, and Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040–903 Ribeirão Preto, São Paulo, Brazil

Correspondence: Address reprint requests to Roosevelt Alves da Silva, E-mail: roos{at}obelix.ffclrp.usp.br.

A new and efficient Monte Carlo algorithm for sampling protein configurations in the continuous space is presented; the efficiency of this algorithm, named Local Moves for Proteins (LMProt), was compared to other alternative algorithms. For this purpose, we used an intrachain interaction energy function that is proportional to the root mean square deviation (rmsd) with respect to -carbons from native structures of real proteins. For phantom chains, the LMProt method is 10⁴ and 20 times faster than the algorithms Thrashing (no local moves) and Sevenfold Way (local moves), respectively. Additionally, the LMProt was tested for real chains (excluded-volume all-atoms model); proteins 5NLL (138 residues) and 1BFF (129 residues) were used to determine the folding success as a function of the number of residues involved in the chain movements, and as a function of the maximum amplitude of atomic displacement r_max. Our results indicate that multiple local moves associated with relative chain flexibility, controlled by appropriate adjustments for and r_max, are essential for configurational search efficiency.