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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. ACEMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software.

Restriction: available to nonprofit users who register using the htmd_register command.
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
a multipurpose Python script for producing plots and user-legible files from the output of AlphaFold2 (notebook) and Colabfold (notebook).
a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
(Adaptive Poisson-Boltzmann Solver) a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE), solves the equations of continuum electrostatics for large biomolecular assemblages.
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.
AutoDock for GPUs and other accelerators, Cuda accelerated version of AutoDock4.2.6. It leverages its parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. The Cuda version was developed in collaboration with Nvidia to run AutoDock-GPU on the Oak Ridge National Laboratory's (ORNL) Summit, and it included a batched ligand pipeline developed by Aaron Scheinberg from Jubilee Development.
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.
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, and classical force fields.
a program for calculating protein electrostatics.

Restriction: available to nonprofit users who register with Columbia & submit confirmation to SBGrid.
a state-of-the-art method for molecular docking
implements fast, high-performance, quantum mechanical and molecular mechanical algorithms in an easy-to-use approach to accelerate drug discovery and development.
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. Dock is offered in the SBGrid collection in …
harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.
a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules.
(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.
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.
a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.
(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.
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
A modern, open library for the analysis of molecular dynamics trajectories
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 for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.
a series of software tools for docking flexible ligands into receptors with selective flexibility, comprising: 1) AutoDockFR: a docking engine using the AutoDock4 forcefield; 2) AutoGridFR: a graphical user interface for setting up docking boxes; 3) 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. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize various models of protein structure with respect to a flexibly defined objective function, …
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
a commandline tool, written in BASH, that sets up and runs a MDFF (molecular Dynamics Flexible Fit) simulation in a semi automatic manner, using only the input PDB file and input density file.
High-resolution de novo Structure Prediction from Primary Sequence
OpenBPMD is an open source implementation of binding pose metadynamics (BPMD).
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.

Restriction: available to academic users who register on the ORCA website / non-profit users who email orca.license@cec.mpg.de or info@faccts.de & submit confirmation to SBGrid.
a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.
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.
an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
a protein structural dynamics analysis software package. ProDy is installed as a module within python.
creates fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.
a threading-based protein structure prediction system.
is a deep learning based protein sequence design method.
a Python library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics (MD) data.
an interactive Python-based interface to the powerful Rosetta molecular modeling suite that 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.
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
accurate prediction of protein structures and interactions using a 3-track network.
a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

Restriction: shared tokens available to non-profit academic labs in North America and Australia as an add-on option
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 fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.
a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.
is an algorithm for sequence independent protein structure comparisons.
a heterogeneous OpenCL implementation of AutoDock Vina.
a parallel molecular docking program that is a modified version of the very popular PC-based molecular docking program AutoDock Vina. VinaLC is a message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.
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.

Restriction: available to users who register with the NIH & submit confirmation to SBGrid.
(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 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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