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Bioinformatics Advance Access originally published online on August 29, 2006
Bioinformatics 2006 22(21):2693-2694; 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

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 and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA
2 Department of Computer Science, University of North Carolina Chapel Hill, NC 27599, USA

*To whom correspondence should be addressed.

Summary: We built 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 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

Contact: dokh{at}med.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on August 14, 2006; revised on August 23, 2006; accepted on August 23, 2006

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