iFold: A platform for interactive folding simulations of proteins

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

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

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 Gō-interactions between amino acids.

Original languageEnglish (US)
Pages (from-to)2693-2694
Number of pages2
JournalBioinformatics
Volume22
Issue number21
DOIs
StatePublished - Nov 1 2006

Fingerprint

Protein folding
Discrete Dynamics
Protein Folding
Molecular Dynamics Simulation
Folding
Molecular dynamics
Proteins
Protein
Molecular Dynamics
Time Scales
Simulation
Denaturation
Frustration
Simulated annealing
Thermodynamics
Simulated Annealing
Length Scale
Computer Simulation
Web-based
Amino Acids

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Sharma, Shantanu ; Ding, Feng ; Nie, Huifen ; Watson, Daniel ; Unnithan, Aditya ; Lopp, Jameson ; Pozefsky, Diane ; Dokholyan, Nikolay V. / iFold : A platform for interactive folding simulations of proteins. In: Bioinformatics. 2006 ; Vol. 22, No. 21. pp. 2693-2694.
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Sharma, S, Ding, F, Nie, H, Watson, D, Unnithan, A, Lopp, J, Pozefsky, D & Dokholyan, NV 2006, 'iFold: A platform for interactive folding simulations of proteins', Bioinformatics, vol. 22, no. 21, pp. 2693-2694. https://doi.org/10.1093/bioinformatics/btl460

iFold : A platform for interactive folding simulations of proteins. / Sharma, Shantanu; Ding, Feng; Nie, Huifen; Watson, Daniel; Unnithan, Aditya; Lopp, Jameson; Pozefsky, Diane; Dokholyan, Nikolay V.

In: Bioinformatics, Vol. 22, No. 21, 01.11.2006, p. 2693-2694.

Research output: Contribution to journalArticle

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Sharma S, Ding F, Nie H, Watson D, Unnithan A, Lopp J et al. iFold: A platform for interactive folding simulations of proteins. Bioinformatics. 2006 Nov 1;22(21):2693-2694. https://doi.org/10.1093/bioinformatics/btl460