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Conformational transition modeling software tools | Protein structure data analysis

The decryption of transient structural changes during protein conformational transitions is essential to a detailed understanding of protein functions. To this end, coarse-grained protein structural models have proven valuable by enabling…
iMODS
Web

iMODS

Facilitates the exploration of such modes and generates feasible transition…

Facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures. iMODS supports advanced visualization capabilities for illustrating collective…

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KGS
Desktop

KGS Kino-Geometric Sampling

Provides an RNA conformational morphing procedure. KGS is all-atom algorithm to…

Provides an RNA conformational morphing procedure. KGS is all-atom algorithm to compute motions of conformational change directly and exactly in the secondary structure constraint manifold between…

MinActionPath
Web

MinActionPath

Combines the action minimization formalism and the Elastic Network Model (ENM)…

Combines the action minimization formalism and the Elastic Network Model (ENM) to generate trajectories between two known structural states of a given macromolecule. MinActionPath works if the…

ANMPathway
Web

ANMPathway Anisotropic Network Model Pathway

Constructs a physically reasonable pathway between two endpoints of a…

Constructs a physically reasonable pathway between two endpoints of a conformational transition. ANMPathway represents a direct application of the “string method” to a two-state coarse-grained…

aANM
Desktop

aANM adaptive Anisotropic Network Model

Elucidates the transition mechanisms in such supramolecular systems.…

Elucidates the transition mechanisms in such supramolecular systems. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimization algorithm, and…

Climber
Desktop

Climber

Pulls interresidue distances of a given conformation towards the distances in…

Pulls interresidue distances of a given conformation towards the distances in the target final conformation using a set of harmonic restraints. In this morphing method, the restraining energy depends…

NMSim
Web

NMSim

A normal mode-based geometric simulation approach for exploring biologically…

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. The approach has been shown to reproduce experimentally observed…

GOdMD
Web

GOdMD

A web app to trace conformational transitions in proteins. GOdMD uses the fast…

A web app to trace conformational transitions in proteins. GOdMD uses the fast CG dMD algorithm coupled to two biasing methods: (i) metadynamics adapted to follow proteins easiest deformation…

MD-dMD
Web

MD-dMD Maxwell-Demon discrete Molecular Dynamics

A web app for determining pathways for conformational transitions in…

A web app for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics, and biasing techniques based on a combination of essential…

PATH-ENM
Web

PATH-ENM

Studies large-scale conformational transitions of proteins between two known…

Studies large-scale conformational transitions of proteins between two known structures. PATH-ENM is based on a mathematically simple form of a mixed potential, whose saddle-point and…

iENM
Web

iENM interpolated Elastic Network Model

Generates a transition pathway between the two protein conformations. The key…

Generates a transition pathway between the two protein conformations. The key idea of iENM is to solve the saddle points of a general double-well potential function constructed from two elastic…

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