Channel detection bioinformatics tools | Protein structure analysis

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Nucleic acids research 5 Bioinformatics 3 BMC bioinformatics 2 PLoS computational biology 2 Proteins 2 International journal of molecular sciences 2 Computers in biology and medicine 1 Nature communications 1 Structure 1 Journal of computational chemistry 1 BMC structural biology 1 Journal of chemical theory and computation 1 Biophysical journal 1 Journal of theoretical biology 1 Journal of molecular graphics & modelling 1 Journal of molecular graphics 1 bioRxiv 1

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Czech Science Foundation 1 European Molecular Biology Organization 1 Howard Hughes Medical Institute 1 Japanese Ministry of Education, Culture, Sports, Science and Technology 1 National Institutes of Health 1 Czech Ministry of Education 1 European Regional Development Fund 1 European Social Fund 1 Grant Agency of the Czech Republic 1 Academia Sinica 1

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CAVER

(1)

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 materials. CAVER can be used either as PyMol plugin or independent application CAVER Analyst. CAVER Analyst has been designed for easy set-up of calculation, visualization of results and efficient data analysis. It can be used for both static structures and molecular ensembles from molecular dynamic simulations or NMR.

MOLE

(2)

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 (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties.

PoreDesigner

Designs constriction region of beta-barrel proteins to any desired pore size and makes it hydrophobic. PoreDesigner offers a python workflow which relies on the mechanically, chemically, and mutationally stable beta-barrel scaffold of outer membrane protein type F (OmpF) as a candidate for synthesizing channel-based membranes, for speedy aqueous-phase separations of specific solutes.

MolAxis

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 medial axis of the complement of the molecule, reducing the problem dimension to two, since the medial axis is composed of surface patches. It is designed to analyze proteins channels, calculate pore dimensions and analyze atom accessibility.

3V / Voss Volume Voxelator

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 solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 A for water).

SLITHER

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 an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein.

BetaCavityWeb

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 reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex.

IonchanPred

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 discriminate between ion channels and non-ion channels, distinguish between voltage-gated ion channels and ligand-gated ion channels and predict sodium, potassium, calcium and anion voltage-gated channels.

PoreLogo

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 eventually predict their selectivity. PoreLogo is an automatic tool for analysing, visualizing and comparing the amino acid composition of transmembrane channels and its conservation across the corresponding protein family.

CCCPP / Computes Cavities, Channels, Pores and Pockets in proteins

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 shape of the ligand.

trj-cavity

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 framework for the rapid identification and characterization of cavities detected within MD trajectories. It is also optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, protein channels.

PoreWalker

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 identified and optimised using geometric criteria, and then the biggest and longest cavity through the channel is detected. Finally, pore features, including diameter profiles, pore-lining residues, size, shape and regularity of the pore are calculated, providing a quantitative and visual characterization of the channel.

CHUNNEL

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 analyze large sets of real proteins.

GCMC/BD

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 channel proteins. This is a method used to maintain the desired electrochemical conditions in the boundaries (buffer regions) of the simulation system which are in (equilibrium) contact with the bulk. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems.

iVKC-OTC

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 feature selection technique into the general form of pseudo-amino acid composition to identify six subfamilies of voltage-gated K+ channels (VKCs). One of the remarkable advantages of introducing the optimized tripeptide composition is being able to avoid the notorious dimension disaster or over fitting problems in statistical predictions.

PROPORES

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, “PoreTrace” for pore axes determination and “GateOpen” for opening the gate between neighboring pores. “PoreID” is a grid-based method that avoids orientation dependency of the results. It targets all kinds of pores (pockets, cavities and channels) and is automatic so that only the PDB file of the target protein has to be specified by the user.

HOLLOW

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 surfaces of protein structures.

PrinCCes / Protein internal Channel & Cavity estimation

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. The decomposition is based on continuity. An individual void is defined by uninterrupted extension in space: a spherical probe can freely move between any two internal locations of a continuous void. Continuous voids are detected irrespective of their topological complexity, they may contain any number of holes and bifurcations. The voids of a protein can be visualized one by one or in combinations as triangulated surfaces.

HOLE

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 to find the best route for a sphere with variable radius to squeeze through the channel.

Panama

Simulates electrophysiology of 11 different types of ion channels via Hodgkin-Huxley style differential equations. Panama assists users to create the response of whole-cell or single-channel parameters to electrical of pharmacological stimuli. It can simulate ion channels (such as among others, voltage-gated sodium, potassium, or chloride channels) under both current clamp and voltage clamp conditions.

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PyMOL 2 CAVER 2 AMBER 1 trj-cavity 1 VMD 1 GROMACS 1 ANM 1

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Unix/Linux 3 Mac OS 3 Windows 3

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Command line interface 3 Graphical user interface 2 Web user interface 1

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C 2 C++ 2 Python 1 Fortran 1

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Neural Tube Defects 1 Nervous System Malformations 1 Substance-Related Disorders 1

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Homo sapiens 2 Saccharomyces cerevisiae 1

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Amino Acids, Dicarboxylic 1 Excitatory Amino Acids 1 Ribonucleotides 1 Heterocyclic Compounds, 2-Ring 1 Purine Nucleotides 1 Amino Acids, Acidic 1 Carbon 1 Hydrocarbons, Acyclic 1 Terpenes 1 Physiological Effects of Drugs 1

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Characterization of the Channel Constriction Allowing the Access of the Substrate to the Active Site of Yeast Oxidosqualene Cyclase

Tools (3): ANM, CAVER, PyMOL

Topics (5): Protein structure analysis, Saccharomyces cerevisiae, Substance-Related Disorders, Hydrocarbons, Acyclic, Terpenes

Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response

Tools (3): GROMACS, VMD, trj-cavity

Topics (4): Protein structure analysis, Homo sapiens, Neural Tube Defects, Nervous System Malformations

Analyses of the Binding between Water Soluble C60 Derivatives and Potential Drug Targets through a Molecular Docking Approach

Tools (3): AMBER, CAVER, PyMOL

Topics (11): Protein structure analysis, Homo sapiens, Carbon, Physiological Effects of Drugs, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Amino Acids, Dicarboxylic, Excitatory Amino Acids, Amino Acids, Acidic, Carbon

Channel identification software tools | Protein structure data analysis