title: iFold: a platform for interactive folding simulations of proteins.
abstract: 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
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA.
authors.forename: Shantanu
authors.initials: S
authors.lastname: Sharma
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Huifen
authors.initials: H
authors.lastname: Nie
authors.forename: Daniel
authors.initials: D
authors.lastname: Watson
authors.forename: Aditya
authors.initials: A
authors.lastname: Unnithan
authors.forename: Jameson
authors.initials: J
authors.lastname: Lopp
authors.forename: Diane
authors.initials: D
authors.lastname: Pozefsky
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: 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
chemical_list: D011506:Proteins