Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions.
This project provides a tool for efficient conformational sampling of protein structures under low resolution restraints. Low resolution electron density maps obtained from, e.g., electron microscopy, as well as distance restraints obtained from NMR or FRET experiments can be used to guide the sampling.
Keywords: CryoEM, flexible fitting, Low-resolution, protein modeling, Structure refinement
Force Field X is a group of open source (GPL v. 3), platform independent (Java Runtime Environment) modules for molecular biophysics. Key methods include:
Polarizable AMOEBA force fields
Particle-mesh Ewald electrostatics
Generalized Kirkwood continuum electrostatics
X-ray and neutron crystallography refinement
Real space refinement for CryoEM
Methods for structure based drug design
Keywords: crystallography, force field, molecular dynamics
This project is a Matlab toolbox for quantifying stability of human movement based on dynamic systems theory. The primary focus is on functions for analyzing stability from experimental data. A secondary focus is to provide functions for analyzing stability of simulations of dynamic systems. For example, quantifying stability of forward dynamic simulations of human walking.
These programs analyze chemical structure and assign force field parameters suitable for the AMBER molecular mechanics/dynamics programs. OpenEye toolkits provide the cheminformatics infrastructure. These programs are intended to be replacements for the programs antechamber and parmchk distributed as part of AmberTools.
Keywords: AMBER, cheminformatics, force field, software tools
This project is for utility programs, beta releases, and data sets that are made available to select OpenSim users, but that are not of interest to the entire OpenSim community.
Keywords: beta releases, OpenSim, plugins, utilities
This project contains a utility program (OpenSMAC) that converts motion files from a Motion Analysis Corp. system (TRB and ANB files) into a format supported by OpenSim (MOT). It can also convert C3D files if you have a valid license and hardware key for SIMM and the Motion Module.
Keywords: ANB import, Motion Analysis, OpenSim, OpenSMAC, TRB import