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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.
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.
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.
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.
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.
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).
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.
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.
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.
MovieMaker
Allows users to create movies of protein folding/unfolding. MovieMaker assists users in generating realistic, downloadable animations of protein motions that can be used by non-specialists for a variety of educational or instructive purposes. This program supports several types of animation: (1) simple rotation, (2) morphing between two end-state conformers, (3) small-scale vibrations, (4) small molecule docking, (5) self-assembly or oligomerization, (6) mid-scale (structure ensemble) motions and (7) protein folding/unfolding.
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.
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.
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.
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.
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.
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.
OPLS3
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 reproduce liquid state thermodynamic properties for a variety of small organic molecules. This tool is a new generation of models based on the Optimized Potentials for Liquid Simulations (OPLS) force field. It can demonstrate that the accuracy of protein-ligand binding affinity is systematically improved by improving of this force field.
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.
Almost / All atom Molecular Simulation Toolkit
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 determination protocols that make use of experimental observables as conformational restraints. To achieve its objectives, Almost has been designed with a flexible architecture, consisting of three application layers : (i) core data structures for the computational representation of molecules, (ii) core algorithms required for an efficient calculation of energies and interaction forces, (iii) methods and algorithms for the structural analysis and assessment of structures and trajectories.
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.
MAVENs / Motion Analysis and Visualization of Elastic Networks
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 the steps. Models can be constructed from raw PDB files or density maps, using all available atomic coordinates or by employing various coarse-graining procedures. Visualization can be performed either with our software or exported to molecular viewers. Mixed resolution models allow one to study atomic effects on the system while retaining much of the computational speed of the coarse-grained ENMs. Analysis options are available to further aid the user in understanding the computed motions and their importance for its function.
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