Flexibility detection software tools | Protein structure data analysis
The mobility of a residue on the protein surface is closely linked to its function. The identification of extremely rigid or flexible surface residues can therefore contribute information crucial for solving the complex problem of identifying functionally important residues in proteins.
Improves accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins. CHARMM36m come from the all-atom additive CHARMM36, a protein force field widely used in molecular modeling and simulations. This tool was found to generate a high population of left-handed α-helix (αL), inconsistent with NMR spectroscopy and small-angle X-ray scattering (SAXS) experimental measurements. The improve version is based on a refined backbone CMAP potential8 derived from reweighting calculation and a better description of specific salt bridge interactions.
Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a remote Web server. This tool is a complete solution for Intranet protein sequence analysis for universities, biological research institutes or biomedical companies. It permits users to integrate secondary structure predictions within multiple alignment and full interactive editing of alignments.
Assists users with the simulation of structure flexibility of folded globular proteins. CABS-flex provides a simulation engine that allows users to reproduce large-scale conformational transitions of protein systems. It includes three consecutive steps: (i) structural clustering, (ii) model reconstruction to an all-atom representation and (iii) model superimposition, analysis and visualization. This method is available as a standalone program and as a web application.
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.
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).
Predicts protein flexibility by calculating the Random Coil Index (RCI) from backbone chemical shifts and estimates values of model-free order parameters as well as per-residue (root mean square fluctuation) RMSF of nuclear magnetic resonance (NMR) and molecular dynamics (MD) ensembles from the RCI. A standalone main-chain RCI program for Linux can be downloaded.
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.
Predicts local protein structures and protein flexibility from its sequence. PredyFlexy provides a user-friendly web interface that combines predictions for local structure and flexibility. Results can be visualized at the amino acid level through a table and graphics.
Performs rigidity and flexibility analysis of proteins. KINARI-Web is a suite of web tools to analyze, visualize and explore rigidity properties of proteins. The software comprises two phases: (i) data input and curation; and (ii) rigidity analysis and visualization. It can be used to add or remove bonds from a protein’s molecular model and to determine the effect of a ligand on the protein’s rigidity.
Allows modelling of proteins as a body-bar-hinge framework. KINARI-Rigidity is a web application that uses a pebble game algorithm. The software first models the protein according to the specified framework, then builds a special multi-graph, which serves as input to the pebble game algorithm that determines its components in terms of graph sparsity.
Predicts normalized B-values from amino acid sequence. PROFbval handles amino acid sequences (or alignments) as input and outputs normalized B-value and two-state (flexible/rigid) predictions. The server also assigns a reliability index for each prediction. For example, PROFbval correctly identifies residues in active sites on the surface of enzymes as particularly rigid.
Generates structure ensembles based on geometrical considerations and has been successfully applied to predict protein conformational flexibility and essential degrees of freedom. A graphical user interface (GUI) has been developed for tCONCOORD, which substantially facilitates the simulation setup and provides valuable insights into the structure analysis and constraint definition process in tCONCOORD.
Allows computation of the normal modes of the structure-based model of a protein of known structure in the space of torsion angles. TNM is an elastic network model (ENM) that uses the torsion angles of the protein backbone as degrees of freedom, combining the topology of the native structure with the constraints imposed by the covalent geometry of proteins. The software normal modes enable the reconstruction of the positions of atoms and the definition of different inter-residues interactions.
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.
A web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). FlexServ can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics.
Provides deformability calculations. DFprot is a web application that combines a simple input interface with an implementation. It increases interactivity with a suitable 2D/3D display of the results. The user can view the query structures colored by the predicted deformability. He can also identify the relative flexibility/rigidity of residues and regions of the protein.
Allows users to upload a membrane protein structure or download from a database and choose one or multiple detergent types to generate a preassembled micelle around the protein. CHARMM-GUI Micelle Builder aims to build a protein/micelle complex system for molecular dynamics (MD) simulation. It can be applied to various proteins with different geometries. This tool can be used for simulation studies of various protein/micelle systems to better understand the protein structure and dynamics in micelles.
Predicts hinge movements. Given a single protein structure, HingeProt automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures.
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 PBs sequences; computes a local measurement of entropy, a density map of PBs along the protein sequence and a WebLogo-like representation of PBs. It offers both a Python library and command-line tools.