title: eSBMTools 1.0: enhanced native structure-based modeling tools.
abstract: BACKGROUND
  Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints.
  
  
  RESULTS
  We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2.
  
  
  BACKGROUND
  http://sourceforge.net/projects/esbmtools/.
  
  
  BACKGROUND
  alexander.schug@kit.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Physics and Steinbuch Centre for Computing, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lutz
authors.forename: Claude
authors.initials: C
authors.lastname: Sinner
authors.forename: Geertje
authors.initials: G
authors.lastname: Heuermann
authors.forename: Abhinav
authors.initials: A
authors.lastname: Verma
authors.forename: Alexander
authors.initials: A
authors.lastname: Schug
mesh_terms: D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA