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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…
ANTHEPROT
Desktop

ANTHEPROT

Allows protein sequence analysis. ANTHEPROT is able to interactively couple…

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…

CHARMM36m
Desktop

CHARMM36m Chemistry at HARvard Macromolecular Mechanics 36m

Improves accuracy in generating polypeptide backbone conformational ensembles…

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…

RCI
Web
Desktop

RCI Random Coil Index

Predicts protein flexibility by calculating the Random Coil Index (RCI) from…

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…

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…

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…

PDBFlex
Dataset

PDBFlex

Explores the intrinsic flexibility of protein structures by analyzing…

Explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric unit of the same protein in PDB. PDBFlex allows to…

FLEXc
Web

FLEXc

Improves the accuracy of protein flexibility prediction. FLEXc incorporates…

Improves the accuracy of protein flexibility prediction. FLEXc incorporates sequence and evolutionary information, context-based scores, predicted secondary structures and solvent accessibility, and…

CoDNaS
Dataset

CoDNaS Conformational Diversity of Native State

A collection of redundant crystallographic structures for a given protein…

A collection of redundant crystallographic structures for a given protein extensively linked with structural, biological and physicochemical information. CoDNaS offers a well curated database that is…

CHARMM-GUI…
Web

CHARMM-GUI Micelle Builder

Allows users to upload a membrane protein structure or download from a database…

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…

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…

Dynameomics
Dataset

Dynameomics

Contains simulations of representatives of essentially all known protein folds.…

Contains simulations of representatives of essentially all known protein folds. The database provides an organizing framework, a repository, and a variety of access interfaces for the simulation and…

PredyFlexy
Desktop
Web

PredyFlexy

Predicts local protein structures and protein flexibility from its sequence.…

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…

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…

tCONCOORD
Desktop

tCONCOORD

Generates structure ensembles based on geometrical considerations and has been…

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…

PROFbval
Web

PROFbval

Predicts normalized B-values from amino acid sequence. PROFbval handles amino…

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…

FlexServ
Web

FlexServ

A web-based tool for the analysis of protein flexibility. The server…

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…

HingeProt
Desktop
Web

HingeProt

Predicts hinge movements. Given a single protein structure, HingeProt…

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…

3DMolNavi
Web

3DMolNavi

Uses for intuitively exploring flexible molecular shape retrieval. 3DMolNavi is…

Uses for intuitively exploring flexible molecular shape retrieval. 3DMolNavi is a web-based retrieval and navigation tool for flexible molecular shape comparison. This tool is based on the histogram…

PCDB
Dataset

PCDB

A database of proteins showing conformational diversity. For each protein, the…

A database of proteins showing conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under…

StoneHinge
Web

StoneHinge

An approach for predicting hinges between domains using input from two…

An approach for predicting hinges between domains using input from two complementary analyses of noncovalent bond networks: StoneHingeP, which identifies domain-hinge-domain signatures in ProFlex…

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