Dynamics detection 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. The internal deformations of protein structures have been used successfully to describe components of these time-dependent fluctuations.
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.
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.
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 of ribosomes, tRNA molecules, and mRNA molecules in the cell as fixed quantities because the dynamics of their production and decay are typically slower than those of protein translation. This tool ignores the details of termination, as well as translation errors.
Investigates protein sequence-structure-dynamic relationships. Bio3D is a platform, available through a web application or as a package, that features including inter-conformer relationship mapping with principal component analysis (PCA), and quantitative comparison of predicted internal dynamics across protein families. It assists users in mapping structural dynamic properties of proteins for which PDB structures are available.
Discovers allosteric signatures in protein molecular dynamics (MD) simulations. TimeScapes is able to find and characterize significant conformational changes in simulated biomolecular systems. It can change time-domain information from MD trajectories into spatial heat maps. This tool is useful for electroporation investigations by transforming the temporal time series of simulations into spatial features.
Simplifies structure-based models (SBMs) development. SMOG is a flexible platform that permits users to define or to extend structure-based models without modifying source code. This application also implements automatic coarse-graining by using two templates internally, one atomistic template that is consistent with the input PDB structure, and one coarse-grained template.
Provides a library dedicated to free energy calculations. PLUMED can be used both (i) as a plug-in: it can be incorporated in more than 10 molecular dynamics codes such AmberTools or IPHIGENIE software, and is able to perform either analysis of the dynamics’ features and multiple free energy methods; (ii) as a command-line tool for postprocessing, allowing analysis on trajectories saved in multiple formats.
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.
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.
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).
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.
Assists users in learning about the dynamic and allosteric behavior of biomolecules. DynOmics is a portal that incorporates three essential components: (i) evaluation of collective motions of biomolecules not in isolation, (ii) assessment of key sites potentially implicated in chemical, mechanical, binding or signaling properties of the biomolecular systems and (iii) resolution exchanges between full atomic and CG representations.
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 native state and folding dynamics, (3) the multiple-basin model for conformational change dynamics, and (4) the elastic network model for quasiharmonic fluctuations around the native structure. It allows to treat ligands explicitly or implicitly.
Allows an on-the-fly interchange between the atomistic (AT) and grand canonical (CG) description (and vice versa) of the molecules according to their position in space. AdResS is a method that permits users to control basic thermodynamic and structural properties in the transition region.
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.
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 RDC data for simultaneous structure characterization and identification of dynamics of proteins and polypeptides. It also incorporates advanced programming concepts such as class based programming.
A Python package for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics.
Enables molecular dynamics simulations of biomolecular systems. NAMD has been designed to permit continuous software development in view of ever-changing technologies, to utilize parallel computers of any size effectively via message driven computation, to run well on platforms from laptops and desktops to parallel computers with thousands of processors. The most essential feature is Tool Command Language scripting capability, which has been used to implement, e.g., replica exchange dynamics, adaptive biasing forces, and advanced phase space sampling protocols.
Changes the molecular configurations found at a time delay τ along the simulation trajectories. VAMPnet is based on a neural network architecture that can be trained by maximizing a variational approach for Markov processes (VAMP) variational score. It combines the tasks of featurization, dimension reduction, discretization, and coarse-grained kinetic modelling. This tool employs two network lobes to proceed.
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 files, save or plot numerical results without writing any code. You can read the output files and resume analysis in your favorite software.