iFold: a platform for interactive folding simulations of proteins.
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 p(fold) analysis using DMD and coarse-grained protein model with structure-based Gō-interactions between amino acids.


BACKGROUND
http://ifold.dokhlab.org
Sharma
Shantanu
S
Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA.
Ding
Feng
F
Nie
Huifen
H
Watson
Daniel
D
Unnithan
Aditya
A
Lopp
Jameson
J
Pozefsky
Diane
D
Dokholyan
Nikolay V
NV
D000595:Amino Acid Sequence; D003198:Computer Simulation; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D011506:Proteins