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Directors: Altman, Russ, M.D., Ph.D.; Delp, Scott, Ph.D.


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.





  • DireX - Conformational Sampling under Low Resolution Restraints ( Software )

    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 ( Software )

    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

  • Matlab Stability Toolbox Focused on Human Movement ( Software )

    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.

  • OEAntechamber assign and generate AMBER atom types and structural parameters ( Software )

    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

  • OpenSim Utilities and Beta Releases ( Software )

    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

  • OpenSMAC: Utility for importing Motion Analysis data (TRB, ANB) into OpenSim ( Software )

    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

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Last updated: 2013-10-01T15:56:29.685-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016