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DynaMine

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 short peptides. It can predict backbone flexibility at the residue-level in the form of backbone N-H S2 order parameter values. The tool is able to distinguish regions of different structural organization for proteins covering a broad range of distinct structural and functional properties.

iGNM

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 2.0 covers more than 95% of the structures currently available in the PDB. Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.

UNRES / UNited RESidue

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 per residue are present. Owing to this reduction, it offers ~1000-4000-fold speed up in molecular dynamics simulations compared to all-atom approaches. With recently introduced parallelization of energy and force evaluation, it enables us to perform ab initio folding simulations of 200-residue proteins in hours and simulations of large biologically important conformational changes in large proteins (e.g., molecular chaperones) in days of wall-clock time.

JED / Java Essential Dynamics

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 Principal Component Analysis (dpPCA) on a selected subset where no alignment required for dpPCA. The tool is able to eliminate outliers, dpPCA by using the Z-score and can calculate cumulative overlap (CO), root mean square inner product (RMSIP), and principal angles (PA).

Bio3D-web

A web application that implements a complete workflow for user customized investigation of protein sequence-structure-dynamic relationships. Bio3D-web provides unparalleled online functionality including inter-conformer relationship mapping with principal component analysis (PCA), and quantitative comparison of predicted internal dynamics across protein families via new ensemble normal mode analysis (eNMA). Together with conventional sequence and structure analysis methods these approaches allow researchers to map the structural dynamic properties of proteins for which PDB structures are available.

HTMD / High-Throughput Molecular Dynamics

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 different levels while abstracting implementation details and best-practice knowledge. Its functionalities range from molecular structure manipulation to system building, docking, Molecular Dynamics (MD) simulations, simulation management, clustering, Markov models, and adaptive sampling.

SeekR / Simulation Enabled Estimation of Kinetic Rates

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 theory. SeekR can be used to run predictive multi-scale milestoning calculations. It uses a multi-scale MD/BD/milestoning methodology to examine ligand-protein binding events. The tool aids the user in running simulations locally and on supercomputers.

FFNCAA / Forcefield_NCAA

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 forcefield parameters calculated and derived for FF_NCAA. With a user submission, the interface performs the requested modifications and minimizes the structure to remove any clashes that have been formed by introducing the non-canonical amino acid to the nearest local minimum.

KOSMOS

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 or transient pathway generation by simply submitting Protein Data Bank (PDB) ID or uploading personal data files through the query page. All the simulation outputs have been deposited into Normal Mode Analysis (NMA) and Elastic Network Interpolation (ENI) database where most of data are disclosed to the public unless users request to limit accessibility to their data. Users can also enjoy versatility of KOSMOS through advanced query by utilizing several unique applications of elastic network models for their own purpose.

iMODS

Facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. Several optimizations have been applied to iMod for supporting online service: (i) the method has been improved, including the implementation of a faster eigenproblem solver, (ii) an affine-modelbased approach has been implemented to facilitate normal mode visualization, and (iii) the simulation of conformational transition trajectories has been extended to address homologous structures.

MDLovoFit

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 structures. A Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations.

MSMBuilder / Markov State Models Builder

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 dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov State Models (MSMs), a class of models that has gained favour among computational biophysicists. In addition to MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models (HMMs) and time-structure based independent component analysis (tICA). MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python API (application programming interface).

AMBER / Assisted Model Building with Energy Refinement

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 parameterize more complex molecules and fragments not currently present in the force field libraries. The suite can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

Cyclo-lib

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 includes 70 cyclodextrins typically employed for fundamental and industrial research. Tools for comparative analysis between different cyclodextrins, as well as to restrict the analysis to specific time-segments within the trajectories are also available. Cyclo-lib provides not only the most probable structures and a detailed analysis of a large number of CDs in aqueous solution but also the parameter files required to perform more complex simulation studies including docking, aggregation or adsorption to interfaces.

GROMACS

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Performs molecular dynamics simulations and energy minimization. GROMACS provides a rich set of calculation types, preparation and analysis tools. It also distributes computational work across ensembles of simulations, multiple program paths and domains within simulations, multiple cores working on each domain, exploiting instruction-level parallelism across those cores handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in.

SMOG / Structure-based Models for Biomolecules

A downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use structure-based models (SBMs) with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications.

WESTPA / Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Allows weighted ensemble (WE) simulation and analysis. WESTPA is an interoperable, scalable software package that embodies the full range of WE’s capabilities. The software is designed to run WE simulations efficiently while exploiting the strengths of WE sampling. It supports simulation of equilibrium, non-equilibrium steady-state, and relaxation processes. WESTPA can be used with any typical scientific computing platform, including desktop workstations, commodity clusters, and supercomputers, and can automatically take advantage of accelerator technologies like graphics processing units (GPUs) or other coprocessors.

ElNemo

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 of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNemo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNemo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors).

distanceP

Predicts distance constraints that correlate well with the observed distances in proteins. distanceP performs better than simple statistical data-driven approaches. It was evaluated and the results show that the information content of the logos has the same qualitative behavior as the network performance for increasing sequence separation. The tool can be combined with a structure prediction method in order to give a significant performance improvement on the short sequence separations.

ANM / Anisotropic Network Model

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 structures. The new version (ANM 2.0) allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein–DNA/RNA and –ligand systems. It offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces.

WebPSN

Employs a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy to investigate allosterism in biological systems. WebPSN allows the user to easily setup the calculation, perform post-processing analyses and both visualize and download numerical and 3D representations of the output. Speed and accuracy make this server suitable to investigate structural communication, including allosterism, in large sets of bio-macromolecular systems.

NMSim

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. The approach has been shown to reproduce experimentally observed conformational variabilities in the case of domain and loop motions and is able to generate meaningful pathways of conformational transitions. The generated structures are of good stereochemical quality. Thus, they can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.

NOMAD-Ref

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 programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions.

BOCS / Bottom-Up Open-Source Coarse-Graining Software

Allows parameterizing of bottom-up coarse-grained (CG) models. BOCS is a toolkit, based upon the generalized Yvon-Born-Green (g-YBG) framework, that provides tools for interpreting the physical origin of these potentials in terms of structural correlations generated by the high-resolution model. It includes (1) software for use with the GROMACS43,44 and LAMMPS45 simulation packages, (2) a stable implementation of the MS-CG force-matching method for determining CG potentials directly from atomistic forces, and (3) the g-YBG framework for calculating MSCG potentials directly from structural data.

PreFRP

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 a web server that provides a method to visualize fluctuation residues in different colors. The information provided by the web server may help the user to carry out further structural and conformational analysis on proteins. Furthermore, the probability scores provided on the results page are very helpful for users who wish to perform docking, mutation, or dynamics studies.

WEBnma / Web-server for Normal Mode Analysis of proteins

A web-based server to perform normal modes calculations and different types of analyses. [email protected] allows efficient calculation of normal modes for proteins. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations. [email protected] version 2.0 also provides comparative NMA on multiple protein structures.

AD-ENM / Analysis of Dynamics of Elastic Network Model

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 (or CA atoms within certain distance cutoff) by springs with a uniform force constant. For DNA/RNA structures P atoms are used instead to build the ENM. Then a normal modes analysis is executed to yield a spectrum of normal modes for the ENM. The low-frequency end of the spectrum is particularly interesting because those lowest modes are able to capture collective conformational changes that are hard to access by all-atom molecular dynamics simulations.