title: Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates.
abstract: We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data.
authors.affiliation: Kansas State University, Manhattan, KS, USA.
authors.forename: Weihong
authors.initials: W
authors.lastname: Zhang
authors.affiliation: NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA.
authors.forename: Steven C
authors.initials: SC
authors.lastname: Howell
authors.affiliation: Centre for Computational Science, Department of Chemistry, University College London, 10 Gordon St., London, UK.
authors.forename: David W
authors.initials: DW
authors.lastname: Wright
authors.affiliation: James Madison University, Department of Chemistry & Biochemistry, Harrisonburg, VA, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Heindel
authors.affiliation: Department of Physics, The George Washington University, Washington, DC, USA.
authors.forename: Xiangyun
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Kansas State University, Manhattan, KS, USA. Electronic address: jianhanc@ksu.edu.
authors.forename: Jianhan
authors.initials: J
authors.lastname: Chen
authors.affiliation: NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA. Electronic address: joseph.curtis@nist.gov.
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Curtis
mesh_terms: D002241:Carbohydrates / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009696:Nucleic Acids / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
chemical_list: D002241:Carbohydrates; D009696:Nucleic Acids; D010455:Peptides; D011506:Proteins; D012997:Solvents; D004247:DNA
keywords: Monte Carlo; SANS; SAXS; Small-angle scattering; Structural biology; Torsion angle molecular dynamics