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a heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. It is extremely fast (115ns/day for DHFR using 1 GPU) and performs MD simulations on the microsecond scale in a single workstation. ACDMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software. ACEMD is freely available to ...
consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models
a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst and enhanced by several others.
a "pipeline" for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images or particle stacks using a set of provided tools. Appion consists of a web-based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed ...
a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.
a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
a method to generate protein conformations around a known structure based on geometric restrictions.
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6 ...
a program for calculating protein electrostatics.

DelPhi is freely available to non-profit labs, but each lab must register with Columbia before we can install the software. To include this software in your installation, please register here https://bhapp.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi, then send a copy of your registration confirmation to us at licensing@sbgrid.org.

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized.
(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.
computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself. The HYDROPRO calculation comprises the basic hydrodynamic properties: translational diffusion coefficient, sedimentation coefficient, intrinsic viscosity, and relaxation times, along with the ...
a toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.
(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.
a software package comprised of AutoDockTools (ADT), Python Molecule Viewer (PMV) and a python programming environment called Vision, developed for visualization and analysis of molecular structures.

AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

PMV is a powerful ...

A series of software tools pertaining to docking flexible ligands into receptors with selective flexibility. AutoDockFR: a docking engine using the AutoDock4 forcefield AutoGridFR: a graphical user interface for setting up docking boxes AutoSite: a ligand binding site detection and characterization program
(Metropolis Monte Carlo) a program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various ...
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
An electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: Adding a limited number of missing heavy atoms to biomolecular structures; Determining side-chain pKas; Placing missing hydrogens; Optimizing the protein for favorable hydrogen bonding; Assigning charge and radius parameters ...
an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.
a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.
a protein structural dynamics analysis software package. ProDy is installed as a module within python.
a threading-based protein structure prediction system.
an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
software for macromolecular electrostatics. Qnifft is available to academic users, but each lab must download the software from the Qnifft website before we can install the software. To include this software in your installation, please download the software here http://crystal.med.upenn.edu/software.html, then send us an email at licensing@sbgrid.org.
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
a suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to it’s size, it is not included in our default installation. To add Schrördinger to your installation, please email bugs@sbgrid.org. Use of the Schrodinger Molecular Modeling Suite through SBGrid is limited to nonprofit groups located in the US and Canada. Members ...
a program for prediction of protein side-chain conformations.
a program for prediction of protein side-chain conformations.
a collection of utilities designed to help setting up and analyze molecular simulations.
a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure; allows efficient computation of boundary forces as required in molecular dynamics simulations; guarantees a minimal solute-boundary-distance; allows to specify a minimum solvent surface curvature in order to avoid `flat' surface ...
offers protein fold recognition by optimal protein sequence threading. THREADER is freely available to non-profit labs, but each lab must register with University College London before we can install the software. To include this software in your installation, please register here http://bioinf.cs.ucl.ac.uk/web_servers/psipred_server/obtain_threader_3_licence, then send a copy of your registration confirmation to us at licensing@sbgrid.org.
a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints. vmd-xplor is freely available to non-profit labs, but each lab must register with ...
(Yammp Under Python) a molecular modeling program designed as a general purpose tool, although development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp. Also known as Yammp 2.
a full rigid-body search of docking orientations between two proteins.
a free database of commercially-available compounds for virtual screening. ZINC contains over 21 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility. The dataset was compiled by David Wrobel (ICCB-Longwood) for in silico docking. The date-stamped datasets are available in /programs/share/iccb.
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