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Bioinformatics Advance Access published online on August 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl460
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 14, 2006
Accepted August 23, 2006

Applications note

iFold: a platform for interactive folding simulations of proteins

Shantanu Sharma 1, Feng Ding 1, Huifen Nie 1, Daniel Watson 2, Aditya Unnithan 2, Jameson Lopp 2, Diane Pozefsky 2, and Nikolay V. Dokholyan 1 *

1 Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
2 Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA

* To whom correspondence should be addressed.
Nikolay V. Dokholyan, E-mail: dokh{at}med.unc.edu


  Abstract

Summary: We built iFold to be a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge to the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and pfold analysis using DMD and coarse-grained protein model with structure-based Go-interactions between amino acids.

Availability: http://ifold.dokhlab.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano
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