Simulation

 

  • Bluues - Electrostatic properties of proteins based on generalized Born radii - online
  • DelPhiForce - electrostatic forces and energy calculations and visualization between two objects
  • MDWeb - Standard protocols to prepare structures, run standard molecular dynamics simulations - online
  • SMPBS - Size Modified Poisson-Boltzmann Solvers is a web server for computing biomolecular electrostatics - online
  • GROMACS - MD simulations using the GROMACS web server - online
  • DelPhiPKa - A web server for predicting pKa of proteins, RNAs and DNAs - online
  • locPREFMD - Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD - online
  • PreFRP - Prediction and visualization of fluctuation residues in proteins - online
  • Mollack - A web server for the automated creation of conformational ensembles for intrinsically disordered proteins - online
  • HTMD - A molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems - standalone
  • Pcetk - A pDynamo-based Toolkit for Protonation State Calculations in Proteins - standalone
  • OREMPRO - Orientation and assessment of atomistic and coarse-grained structures of membrane proteins - online
  • ProtPOS - Prediction of Protein Preferred Orientation on a Surface - standalone
  • 3Drefine - An interactive web server for efficient protein structure refinement - online
  • MemGen - Membrane generator server - online
  • CGmodel - A Coarse-Grained Physical Model for RNA - standalone
  • CONFOLD - Residue-residue contact-guided ab initio protein folding - online
  • PLUMED - An open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. See also binding pocket analysis JEDI - standalone
  • FoldNucleus - Web server for the prediction of RNA and protein folding nuclei from their 3D structures - online
  • Simulation - GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. ProDy is a free and open-source Python package for protein structural dynamics and sequence evolution analysis - standalone
  • RRDistMaps - A UCSF Chimera tool for viewing and comparing protein distance maps - standalone
  • MODA - Membrane optimal docking area. A tool to predict online potential membrane binding site on a protein 3D structure - online
  • WESTPA - An interoperable, highly scalable software package for weighted ensemble simulation and analysis - standalone
  • GDFuzz3D - A method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function - online
  • Polyphony - Superposition independent methods for ensemble-based drug discovery. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates. New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package - standalone
  • DynaMine - The DynaMine webserver: predicting protein dynamics from sequence - online
  • MMC - Monte Carlo program. Simulation of proteins, membrane, prediction of water position... - standalone
  • Wordom - Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of molecular structure and dynamics analysis - standalone
  • Desmond - A software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters - standalone
  • smog-server - The smog-server webtool interface that will give you all the necessary information for performing structure-based simulations of proteins, nucleic acids, as well as many supported ligands (Gromacs) - online
  • HingeProt - HingeProt: Automated Prediction of Hinges in Protein Structures - online
  • iENM - iENM server uses interpolated elastic network model to generate a transition path between two given macromolecular structures - online
  • PATH-ENM - PATH-ENM server uses a newly developed mixed elastic network model (MENM) to generate transition paths between two given macromolecular structures - online
  • kosmos - KOSMOS is the first web server to provide the structural biology community with both harmonic and anharmonic analyses of macromolecular structures including DNA, RNA, and Proteins - online
  • tmm@ - TMM@: a web application for the analysis of transmembrane helix mobility - online
  • FlexServ - FlexServ is a project aimed to show in an easy and visual way flexibility-related properties of proteins. The available types of simulation include Normal Mode Analysis, Brownian Dynamics and Discrete Dynamics - online
  • anm - Anisotropic Network Model web server - online
  • Molmovdb - Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis - online
  • pDynamo - Simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions (see also for Mac GTKDynamo) - standalone
  • PackMol - Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. Might be used to build a membrane... - standalone
  • Abalone - Abalone is a Molecular Mechanics Software open source project on sourceforge.net. Its primary use is for studying macromolecular systems, esp. peptides, by molecular mechanics, molecular dynamics, and monte carlo (Windows XP) - standalone
  • MSMBuilder - MSMs are a powerful means of modeling the structure and dynamics of molecular systems, like proteins - standalone
  • iMODS - To explore the collective motions of proteins and nucleic acids using NMA in internal coordinates (torsional space) just submit the PDB-ID or the atomic coordinates in PDB format (3.x). Backbone atoms N, CA and C are mandatory for dihedral angles definition - online server (2014)
  • Climber - A non-linear protein trajectory morphing method - standalone
  • ForceBalance - Systematic Force Field Optimization - standalone
  • NAST - The Nucleic Acid Simulation Tool - standalone
  • DireX - Conformational Sampling under Low Resolution Restraints - standalone
  • RosettaBackrub - Flexible backbone protein structure modeling and design server. Can be used for Point mutation, Backbone ensemble (creates near-native structural ensembles), Sequence tolerance (predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity) - online
  • Princeton_TIGRESS - Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure - .
  • MemBuilder - A web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program - .
  • GOAP - A generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys. Protein structure quality assessment - Standalone
  • KoBaMIN - A Knowledge Based MINimization Web Server for Protein Structure Refinement - .
  • BCL::Fold - De novo prediction of large proteins by assembly of secondary structure elements - standalone
  • UNRES - A package to carry out coarse-grained simulations of protein structure and dynamics - .
  • MoDEL - Molecular Dynamics Extended Library is a large library of molecular dynamics trajectories of representative protein structures - database
  • EdaFoldAA - A fragment assembly based de novo protein structure prediction method that uses an Estimation of Distribution Algorithm for high efficiency conformational sampling - standalone
  • EdaFold - A C++/MPI software prototype for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures - standalone
  • MORPH-PRO - A novel algorithm and web server for protein morphing Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations - online
  • Vienna-PTM - Web server: a toolkit for MD simulations of protein post-translational modifications - online
  • NAFlex - A web server for the study of nucleic acid flexibility - online
  • NAFlex - A web server for the study of nucleic acid flexibility - online
  • CABS-flex - Server for fast simulation of protein structure fluctuations - online
  • IMAAAGINE - A webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank - online
  • RNAiFold - A web server for RNA inverse folding and molecular design - online
  • RNAstructure - Web servers for RNA secondary structure prediction and analysis - online
  • SPARCS - Web server to analyze (un)structured regions in coding RNA sequences - online
  • GalaxyRefine - Protein structure refinement driven by side-chain repacking - online
  • 3DEM Loupe - Analysis of macromolecular dynamics using structures from electron microscopy - online
  • PELE - Protein Energy Landscape Exploration, is based on protein structure prediction algorithms and a Monte Carlo sampling and is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques - online
  • Wolf2Pack - Portal Based Atomistic ForceField Development - standalone and online
  • Smina - A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization - standalone
  • ALADYN - Dynamics-based alignment of proteins (The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. The latter often accompany functional conformational changes in proteins and enzymes. The ALADYN dynamics-based alignment can therefore highlight functionally-oriented correspondences that could be more elusive to sequence or structure-based comparisons) - online
  • Link - Radius of Gyration - online
  • CHARMM-GUI - The Ligand Binder helps the user generate a series of CHARMM inputs to calculate a protein/ligand binding free energy - Online tools for Charmm
  • iBIOMES - Disseminating simulation data to create knowledge - Simulation, standalone
  • Link - Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores - Simulation, Charmm, Online
  • NMSim - The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes - Simulation online
  • Link - Many tools for structural bioinformatics, loop prediction, simulation, structural refinement of proteins with Gromacs, Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent, small molecules - Structural bioinformatics online
  • CAMPOS - The CAMD Open Software project is a collection of programs for atomic-scale simulations - Simulation tools
  • Link - Local move is a Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers - Simulation tools - Flexibility - Structure Prediction Analysis
  • PredyFlexy - Flexibility and local structure prediction from sequence - .
  • KoBaMIN - A knowledge-based minimization web server for protein structure refinement - .
  • Dynameomics - Continuing project to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation - Simulation
  • iFold - A web portal for interactive protein folding/unfolding simulations... performs discrete molecular dynamics simulations of proteins using coarse-grained structural models - Simulation
  • MD-TRACKS - A collection of command line tools and a python package to facilitate and automate the analysis of molecular dynamics and monte carlo simulations. MD-Tracks is a trajectory analysis toolkit. It is designed to interact with several simulation codes that generate trajectory data: CP2K, CPMD, DLPOLY, GROMACS, LAMMPS. The trajectory output files are first converted into a in a uniform binary format, which can then be processed with a bundle of analysis scripts, e.g. for the analysis of vibrational spectra, diffusion constants, radial distribution functions, and so on - Simulation
  • clickMD - Molecular dynamics in one click (contact the authors) - MD, the online server does not seem to work Nov 7 2013
  • Gromacs - Gromacs molecular modeling - simulation - .
  • ProBLM - (Pro)tein (B)ilayer (L)ipid (M)embrane is a webserver and stand-alone desktop application that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC or POPE) - online and standalone
  • Link - Lipid membrane in 3D - .
  • Tinker - Tinker molecular modeling - simulation - .
  • Towhee - A Monte Carlo molecular simulation - .
  • AMMP - A full-featured molecular mechanics, dynamics and modeling program - .
  • PINY_MD - Capable of performing a wide variety of molecular dynamics - .
  • WEBnm@ - A web application for normal mode analysis of proteins - .
  • PBEQ-Solver - Online visualization of electrostatic potential of biomolecules - Electrostatics
  • Link - pKa calculations with the FD/DH method (Warwicker Group) - Electrostatics, standalone
  • PIPSA - This PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins - Electrostatics
  • PCE - Online tools to compute protein electrostatics based on MEAD (Bashford and Karplus 1990): PCE (Protein Continuum Electrostatics). See PCE pKa and electrostatics - Electrostatics, online
  • H++ - H++, pKa - Electrostatics, online
  • Bluues server - Electrostatic properties of wild-type and mutated proteinS - Electrostatics, online
  • Link - Web servers and services for electrostatics calculations with APBS and PDB2PQR - Electrostatics, online
  • DelPhi - DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol - Electrostatics, online
  • POLYVIEW-MM - Web-based platform for animation and analysis of molecular simulations - online
  • CLICK - Web server for superimposing the 3D structures of any pair of biomolecules - .
  • Link - A web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters - .
  • R.E.D. Server - Web service to automatically derive RESP and ESP charges - .
  • SuperPose - Protein superposition server - .
  • ProPka - Electrostatics - standalone
  • APBS - (Baker et al. 2001): software package for the numerical solution of the Poisson-Boltzmann equation - Electrostatics
  • OOPS - Open Protein Simulator - Molecular simulations
  • WhatIf - Web interface to the versatile molecular modeling package - online, modeling structural analysis
  • elNemo - Elastic Network Model web interface - online
  • elNemo - Web-interface to The Elastic Network Model (Gohlke group, paper by Pfleger et al 2013) - Molecular simulations, online
  • Link - Non covalent bond finder - Structural analysis
  • MODEL - Molecular Descriptor Lab for Computing structural and physichemical properties of molecules from their 3D structures - Molecular Descriptor from 3D
  • SVMProt - Protein functional family prediction - Structural analysis
  • SODIUM - Arrange ions around biological macromolecules - .
  • Link - The Biomolecule Toolkit - Molecular modeling
  • oGNM - (Yang et al. 2006): calculating the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian network Model (GNM) - Molecular simulations, flexibility
  • ProtoMol - Object-oriented component based framework for molecular dynamics simulations - Molecular simulations
  • PDB_Hydro - Tools for mutating and solvating protein structures - .
  • NOMAD-Ref - (Lindahl et al. 2006): Tools using normal modes for structural refinement of large proteins - Molecular simulations
  • FSolv - Fast method for the determination of fractional contributions to solvation in proteins - Solvation
  • ILM - (Ruan et al. 2004): web server combining two algorithms, iterated loop matching and maximum weighted matching, for predicting RNA secondary structures - RNA structure prediction
  • RDfolder - (Ying et al. 2004): webserver for prediction of RNA secondary structure from two methods, random stacking of helical regions and helical regions distribution - RNA structure prediction
  • NAMD - Molecular dynamics package for simulation of large biomolecular systems - Molecular simulations
  • CHARMM - Chemistry at HARvard Molecular Mechanics is a program for macromolecular simulations - Molecular simulations
  • Link - Many perl scripts to analyze a protein, add ions, compute volume, add ions in a box of water, tools for Python, compute energy.. - Analyze protein structures
  • Link - Scripts for manipulating molecules - scripts to help prepare organic molecules for simulation
  • AmberTools12 - Modeling - Analyze protein structures
  • Link - Python macromolecular library..many tools to study PDB files, geometry, viewer... mmLib, Class for least-squares structural superposition... - Analyze protein structures
  • Uppsala Software Factory - Many tools for proteins, statistics about your PDB file, volume... - Analyze protein structures
  • RAPIDO - A web server for the alignment of protein structures in the presence of conformational changes - Analyze protein structures - RMSD
  • Link - superimpose 3D structural superposition server - .
  • PDB2PQR - Server to prepare PDF file - .
  • PRODRG - Will take a description of a small molecule (as PDB coordinates / MDL Molfile / SYBYL Mol2 file / text drawing) and from it generate a variety of topologies for use with GROMACS, WHAT IF, Autodock, HEX, CNS, REFMAC5, SHELX, O and other programs, as well as energy-minimized coordinates in a variety of formats - .
  • Link - This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS - .
  • Link - B is a Java-based, on-line biomolecular modeling package - Molecular modeling
  • GROMACS - (Van Der Spoel et al. 2005) is a package for performing standard MD simulations, energy minimizations, NMR refinement - Molecular simulations
  • Link - Molecular Dynamics Extended Library (Database of Molecular Dynamics Trajectories) - Molecular simulation database
  • Link - The Uppsala Electron Density Server (Kleywegt et al. 2004) - Protein X-ray structural analysis
  • BioShell - A suite of programs designed for pre- and post-processing in protein structure modeling protocols - Tools to prepare molecules for simulations
  • Link - Protein Dipole Moments Server - Electrostatics: dipole moment
  • PAT - A protein analysis toolkit for integrated biocomputing on the web - Structural Analysis
  • PFplus - Patch Finder Plus: A web server for extracting and displaying positive electrostatic patches on protein surfaces - .
  • MORPH - The MORPH server produces 2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations. See also database of macromolecular movements. Receptor flexibility - Structural analysis
  • DFprot - Server provides deformability/flexibily analysis of your 3D structure - Macromolecule Flexibility online
  • AD-ENM - Provides a spectrum of analyses for the dynamics of an elastic network model built from a given macromolecular structure - Macromolecule Flexibility
  • MoViES - Molecular Vibrations Evaluation Server - Macromolecule Flexibility
  • DynDom - A program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available - online, hinge, flexibility
  • Link - An Algorithm For Protein Hinge Prediction Using Elastic Network Models - online, hinge, flexibility
  • KINARI - A suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules - online
  • CNA - Web server: rigidity theory-based thermal unfolding simulations of proteins for Linking structure, (thermo-)stability, and function - online
  • TLSMD - TLS Motion Determination analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions - online, hinge, flexibility
  • MOIL - Molecular Dynamics and Modeling Software - standalone
  • SQUEEZE - A method to reduce the computational cost of simulations of macromolecules performed under periodic boundary conditions. SQUEEZing allows removing the superfluous solvent molecules, by using the shape of the solute as the basis for the unit cell - online
  • Charmming - CHARMM online for simulation(CHARMM INterface and Graphics), small molecules, Ligand docking functionality. SAR and QSAR model building tools. ProPKA support for determining titration states etc - online
  • OpenMM - Open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. (simulations on GPUs and CPUs, see OpenMM Zephyr) - .
  • Ligandbook - A public repository for force field parameters for small drug-like molecules and known ligands of proteins - .
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira