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Channel extraction software tools | Protein structure data analysis

A channel is defined as a hole penetrating a molecular structure with two or more openings toward the exterior space through which a solvent or ligand molecule can freely pass.Source text:(Kim et al., 2015) BetaCavityWeb: a webserver for molecular…
ARAMEMNON
Dataset

ARAMEMNON

A resource designed for scientists, who look for a convenient way to access…

A resource designed for scientists, who look for a convenient way to access data about individual plant membrane proteins and membrane protein families. Currently, ARAMEMNON provides membrane protein…

BetaCavityWeb
Web

BetaCavityWeb

Molecular cavities, which include voids and channels, are critical for…

Molecular cavities, which include voids and channels, are critical for molecular function. BetaCavityWeb computes these cavities for a given molecular structure and a given spherical probe, and…

trj-cavity
Desktop

trj-cavity

Finds protein cavities throughout Molecular Dynamics (MD) simulation…

Finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. trj_cavity can analyse the solvent occupancy of the cavities identified. This tool is implemented within the GROMACS…

SuperPain
Dataset

SuperPain

A database for pain stimulating and pain relieving compounds, which bind or…

A database for pain stimulating and pain relieving compounds, which bind or potentially bind to ion channels, such as TRPV1, TRPM8, TRPA1, hERG, TREK1, P2X, ASIC or voltage-gated sodium channels. The…

CAVER
Desktop

CAVER

Provides rapid, accurate and fully automated calculation of tunnels and…

Provides rapid, accurate and fully automated calculation of tunnels and channels in static structures. The molecules amendable to analysis of CAVER include proteins, nucleic acids or inorganic…

MOLE
Desktop
Web

MOLE

A web-based interactive application for the analysis of access/egress paths to…

A web-based interactive application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of…

SLITHER
Web

SLITHER

A web server that can generate contiguous conformations of a molecule along a…

A web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts…

3V
Desktop
Web

3V Voss Volume Voxelator

Extracts and comprehensively analyzes all the internal volumes from input RNA…

Extracts and comprehensively analyzes all the internal volumes from input RNA and protein structures. 3V rapidly finds internal volumes by taking the difference between two rolling-probe…

MolAxis
Desktop
Web

MolAxis

A tool for the identification of high clearance pathways or corridors which…

A tool for the identification of high clearance pathways or corridors which represent molecular channels in the complement space of proteins. MolAxis is extremely efficient because it samples the…

CCCPP
Desktop

CCCPP Computes Cavities, Channels, Pores and Pockets in proteins

Computes the void parts of the proteins, i.e. cavities, channels and pockets.…

Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the…

CHEXVIS
Web

CHEXVIS

A method for molecular channel extraction based on the alpha complex…

A method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its…

PrinCCes
Desktop

PrinCCes Protein internal Channel & Cavity estimation

A computer program supporting the visualization of voids. PrinCCes includes a…

A computer program supporting the visualization of voids. PrinCCes includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities.…

PoreLogo
Web

PoreLogo

The increasing number of available atomic 3D structures of transmembrane…

The increasing number of available atomic 3D structures of transmembrane channel proteins represents a valuable resource for better understanding their structure-function relationships and to…

PoreWalker
Web

PoreWalker

A fully automated method designed to detect and characterise transmembrane…

A fully automated method designed to detect and characterise transmembrane protein channels from their 3D structure. A stepwise procedure is followed in which the pore centre and pore axis are first…

GCMC/BD
Web

GCMC/BD

Allows one to generate a Brownian dynamics trajectory of ions in a channel…

Allows one to generate a Brownian dynamics trajectory of ions in a channel system. GCMC/BD is a web-based graphical user interface presented for grand canonical Monte Carlo (GCMC) BD simulations of…

CHUNNEL
Desktop

CHUNNEL

An algorithm to automatically find, characterize, and display tunnels or pores…

An algorithm to automatically find, characterize, and display tunnels or pores in proteins. The correctness and accuracy of the algorithm is verified on a constructed set of proteins and used to…

PROPORES
Desktop

PROPORES

A toolkit for identifying pockets, cavities and channels of protein structures.…

A toolkit for identifying pockets, cavities and channels of protein structures. The toolkit was developed in PERL programming language and includes “PoreID” for pore identification,…

HOLLOW
Desktop

HOLLOW

A program that generates a "casting" of the interior volume of the…

A program that generates a "casting" of the interior volume of the protein as dummy atoms. The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior…

HOLE
Desktop

HOLE

A program that allows the analysis and visualisation of the pore dimensions of…

A program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels. The algorithm uses a Monte Carlo simulated annealing procedure…

iVKC-OTC
Web

iVKC-OTC

A sequence-based predictor for identifying the subfamilies of voltage-gated…

A sequence-based predictor for identifying the subfamilies of voltage-gated potassium channels. iVKC-OTC has been developed by incorporating the optimized tripeptide composition (OTC) generated by…

IonchanPred
Web

IonchanPred

Allows identification of ion channels and their types. IonchanPred consists in…

Allows identification of ion channels and their types. IonchanPred consists in a support vector machine-based model employing a feature extraction method called pseudo-dipeptide. The software can…

VKCPred
Desktop

VKCPred

A support vector machine based method was proposed to predict VKC subfamilies…

A support vector machine based method was proposed to predict VKC subfamilies using amino acid and dipeptide compositions. In order to remove redundant information, a novel feature selection…

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