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Dynamics prediction software tools | Protein structure data analysis

Protein dynamics has been described to be the time-dependent changes in the structure of a protein, which includes equilibrium fluctuations governing biological function (Henzler-Wildman and Kern, 2007). The internal deformations of protein…
G T A T C G C T A
SMoPT
Desktop

SMoPT

Describes translation dynamics to the single-nucleotide resolution for entire…

Describes translation dynamics to the single-nucleotide resolution for entire transcriptome. SMoPT is based on a Markov model of translation using the Gillespie algorithm. It treats the total number…

MolMovDB
Dataset

MolMovDB Database of Macromolecular Movements

Allows users to make structural analysis. MolMovDB consists of a set of coupled…

Allows users to make structural analysis. MolMovDB consists of a set of coupled hypertext pages with graphic images and a simple query box. It offers a lot of tools to systematize all instances of…

DynaMine
Web

DynaMine

Allows to make predictions for the fast backbone movements of proteins directly…

Allows to make predictions for the fast backbone movements of proteins directly from their amino-acid sequence. DynaMine returns dynamics profile of a protein sequence that can be computed even for…

REDCRAFT
Desktop

REDCRAFT REsidual Dipolar Coupling Residue Assembly and Filtering Tool

Performs task of backbone structure determination of a protein primarily based…

Performs task of backbone structure determination of a protein primarily based on residual dipolar couplings (RDCs) data. REDCRAFT is an open source analysis tool that accommodates the analysis of…

iGNM
Dataset

iGNM

Hosts a database of output files obtained from running Gaussian network model…

Hosts a database of output files obtained from running Gaussian network model (GNM) calculations on Protein Data Bank (PDB) files and the means for visualizing these files in both 2-D and 3-D. iGNM…

MDAnalysis
Desktop

MDAnalysis

Simplifies the development of analysis tools that specifically make use of the…

Simplifies the development of analysis tools that specifically make use of the widely-used Python language. MDAnalysis facilitates rapid code development which provides a powerful and extensible but…

AQ
Desktop

AQ AQUA-DUCT

Permits to trace, analyze and visualize molecular trajectories throughout…

Permits to trace, analyze and visualize molecular trajectories throughout molecular dynamic (MD) simulations. AQ facilitates the analysis of movement of any small ligand(s) during MD simulations. It…

Bio3D-web
Web
Desktop

Bio3D-web

A web application that implements a complete workflow for user customized…

A web application that implements a complete workflow for user customized investigation of protein sequence-structure-dynamic relationships. Bio3D-web provides unparalleled online functionality…

UNRES
Desktop

UNRES UNited RESidue

A package to carry out coarse-grained simulations of protein structure and…

A package to carry out coarse-grained simulations of protein structure and dynamics. UNRES is a highly reduced protein model; only two interaction sites: united side chain and united peptide group…

JED
Desktop

JED Java Essential Dynamics

Permits to compare the Essential Dynamics (ED) from multiple protein…

Permits to compare the Essential Dynamics (ED) from multiple protein trajectories. JED facilitates comparative studies. It combines native and mutant trajectories and calculates distance pair…

CafeMol
Desktop

CafeMol

Simulates proteins, nucleic acids and protein-nucleic acid complexes. CafeMol…

Simulates proteins, nucleic acids and protein-nucleic acid complexes. CafeMol equips four structure-based protein models: (1) the off-lattice Go model, (2) the atomic interaction based CG model for…

OpenMM
Desktop

OpenMM

A toolkit for molecular simulation using high performance GPU code. OpenMM is…

A toolkit for molecular simulation using high performance GPU code. OpenMM is designed for incorporation into molecular dynamics codes to enable execution on GPUs and other high performance…

HTMD
Desktop

HTMD High-Throughput Molecular Dynamics

Allows the handling of thousands of simulations and multiple systems in a…

Allows the handling of thousands of simulations and multiple systems in a controlled manner. HTMD extends the Python programming language with functions and classes to handle molecular systems at…

IFF
Desktop

IFF INTERFACE Force Field

Enables the accurate simulation of inorganic compounds, biomolecules, and…

Enables the accurate simulation of inorganic compounds, biomolecules, and polymers. IFF provides a collection of all-atom parameters for inorganic compounds that have individually undergone extensive…

iMODS
Web

iMODS

Facilitates the exploration of such modes and generates feasible transition…

Facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures. iMODS supports advanced visualization capabilities for illustrating collective…

SeekR
Desktop

SeekR Simulation Enabled Estimation of Kinetic Rates

Enables researchers to perform multi-scale computation of the kinetics of…

Enables researchers to perform multi-scale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning…

FFNCAA
Web

FFNCAA Forcefield_NCAA

Allows users to upload a PDB structure to be modified by single or multiple…

Allows users to upload a PDB structure to be modified by single or multiple non-canonical amino acids and/or simultaneously mutated. FFNCAA is a web application that permits user to download the…

Evol
Desktop

Evol

A suite of powerful and efficient API features and applications for analysis of…

A suite of powerful and efficient API features and applications for analysis of sequence evolution and its comparison to protein functional dynamics. Evol applications allow you to analyze large MSA…

KOSMOS
Web

KOSMOS

Provides the structural biology community with both harmonic and anharmonic…

Provides the structural biology community with both harmonic and anharmonic analyses of macromolecular structures including DNA, RNA, and Proteins. KOSMOS users can request thermal fluctuation study…

MDLovoFit
Desktop

MDLovoFit

A package for the analysis of the mobility and structural fluctuation in…

A package for the analysis of the mobility and structural fluctuation in Molecular Dynamics simulations. MDLovoFit allows the automatic identification of rigid and mobile regions of protein…

MSMBuilder
Desktop

MSMBuilder Markov State Models Builder

A software package for building statistical models of high-dimensional…

A software package for building statistical models of high-dimensional time-series data. MSMBuilder is designed with a particular focus on the analysis of atomistic simulations of biomolecular…

AMBER
Desktop

AMBER Assisted Model Building with Energy Refinement

Provides numerous programs that work together to setup, perform, and analyze…

Provides numerous programs that work together to setup, perform, and analyze molecular dynamics (MD) simulations. AMBER is a biomolecular simulation package which also contains software designed to…

GSAtools
Desktop

GSAtools

Investigates the conformational dynamics of local structures, the functional…

Investigates the conformational dynamics of local structures, the functional correlations between local and global motions and the mechanisms of allosteric communication. GSATools is a free,…

Cyclo-lib
Dataset

Cyclo-lib

A database with structural and dynamic analysis obtained from computational MD…

A database with structural and dynamic analysis obtained from computational MD simulation trajectories of native and modified cyclodextrins (CDs) in explicit water molecules. Cyclo-lib currently…

Adun
Desktop

Adun

Allows to develop multiple types of simulations. Adun includes all simulation…

Allows to develop multiple types of simulations. Adun includes all simulation levels, that is, micro (all atom molecular dynamics or Monte Carlo), meso (dissipative particle dynamics and related…

Pteros
Desktop

Pteros

Models and analyses molecular dynamics trajectories. Pteros provides a number…

Models and analyses molecular dynamics trajectories. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to…

locPREFMD
Web

locPREFMD local Protein structure REFinement via Molecular Dynamics

Combines minimization, sampling via restrained molecular dynamics and targeted…

Combines minimization, sampling via restrained molecular dynamics and targeted rebuilding of problematic residues to improve the local structural quality of virtually any given protein model. The…

ElNemo
Web

ElNemo

A web interface to the Elastic Network Model that provides a fast and simple…

A web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number…

MODE-TASK
Desktop

MODE-TASK

Analyses and compares protein dynamics obtained from molecular dynamics (MD)…

Analyses and compares protein dynamics obtained from molecular dynamics (MD) simulations and/or coarse grained elastic network models. MODE-TASK allows users to perform standard Principle Component…

ProteinPrepare
Web

ProteinPrepare

Allows the estimation and visualization of charge states. ProteinPrepare is a…

Allows the estimation and visualization of charge states. ProteinPrepare is a web application that offers three main features: (i) help in deciding the protonation state and charge of residues, still…

MD-TASK
Desktop

MD-TASK

Permits the analysis of different properties along Molecular Dynamics (MD)…

Permits the analysis of different properties along Molecular Dynamics (MD) simulations not commonly found in other MD packages. MD-TASK is an easy-to-use tool suite that includes dynamic residue…

PBxplore
Desktop

PBxplore

Uses analysis tools to study protein flexibility and deformability. PBxplore…

Uses analysis tools to study protein flexibility and deformability. PBxplore provides a suite of tools dedicated to Protein Block (PB) analysis. Starting from 3D protein structures, PBxplore assigns…

ProDy
Desktop

ProDy

A Python package for structure-based analysis of protein dynamics. ProDy allows…

A Python package for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally…

ANM
Web

ANM Anisotropic Network Model

One of the simplest yet powerful tools for exploring protein dynamics. Its main…

One of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium…

NMSim
Web

NMSim

A normal mode-based geometric simulation approach for exploring biologically…

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. The approach has been shown to reproduce experimentally observed…

NOMAD-Ref
Web

NOMAD-Ref

Provides tools for online calculation of the normal modes of large molecules…

Provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of…

PreFRP
Web

PreFRP

Extracts sequence and basic information of a protein structure and classifies…

Extracts sequence and basic information of a protein structure and classifies amino acid residues in a protein into three important types like high, moderate and weak fluctuating residues. PreFRP is…

WEBnma
Web

WEBnma Web-server for Normal Mode Analysis of proteins

A web-based server to perform normal modes calculations and different types of…

A web-based server to perform normal modes calculations and different types of analyses. WEBnm@ allows efficient calculation of normal modes for proteins. Starting from a structure file provided by…

AD-ENM
Web

AD-ENM Analysis of Dynamics of Elastic Network Model

Performs analysis of macromolecular dynamics based on a highly simplified…

Performs analysis of macromolecular dynamics based on a highly simplified physical model-Elastic Network Model (ENM): it is built from a given protein structure by connecting its neighboring residues…

Almost
Desktop
Web

Almost All atom Molecular Simulation Toolkit

A molecular dynamics and modeling framework for the determination of the…

A molecular dynamics and modeling framework for the determination of the structure and dynamics of proteins and nucleic acids. Almost aims to provide support for a wide range of different structure…

OPLS3
Desktop

OPLS3

Allows to predict protein-ligand binding affinities with a high accuracy over a…

Allows to predict protein-ligand binding affinities with a high accuracy over a wide rande of targets and ligands. OPLS was one on the first models in which parameters were extensively optimized to…

Discovery…
Desktop

Discovery Studio® Visualizer

A feature-rich molecular modeling environment package for both small molecule…

A feature-rich molecular modeling environment package for both small molecule and macromolecule applications. Discovery Studio® Visualizer is built from, and fully compatible with the latest release…

MDWeb
Web

MDWeb

A personal workspace providing standard protocols to prepare structures, run…

A personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories. The platform provides tools to prepare systems from…

MoDEL
Dataset

MoDEL Molecular Dynamics Extended Library

A large library of molecular dynamics trajectories of representative protein…

A large library of molecular dynamics trajectories of representative protein structures, prepared with the state-of-the-art technology. Basic analyses and trajectories stripped of solvent molecules…

MAVENs
Desktop

MAVENs Motion Analysis and Visualization of Elastic Networks

Aims to bring elastic network models (ENMs) and their analysis to a broader…

Aims to bring elastic network models (ENMs) and their analysis to a broader audience by integrating methods for their generation and analysis into a user friendly environment that automates many of…

gdpc
Desktop

gdpc

Allows visualization of molecular dynamics simulations. gdpc reads xyz input…

Allows visualization of molecular dynamics simulations. gdpc reads xyz input and custom formats, and can write out pictures of the frames.

OPM-DB
Web

OPM-DB

Allows users to explore the protein-membrane systems of the Orientations of…

Allows users to explore the protein-membrane systems of the Orientations of Proteins in Membranes (OPM) built and equilibrated using High-Throughput Molecular Dynamics (HTMD). OPM-DB permits to view…

Oscail
Desktop

Oscail

A windows software for crystallography and molecular modelling. Oscail provides…

A windows software for crystallography and molecular modelling. Oscail provides an integrated high quality system for building and modelling molecules and the system drives Firefly and Tinker. It can…

MoViES
Web

MoViES Molecular Vibrations Evaluation Server

A computer program for computing vibrational normal modes and thermal…

A computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. This software tool was tested on…

Information

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