Herramientas de usuario

Herramientas del sitio


Pocket Detection or Binding Site

SiteHound-web identifies ligand binding sites by computing interactions between a chemical probe and a protein structure.

SiteHunter: is an automated webserver for the prediction of protein-ligand and protein-DNA interactions through protein threading.

POCASA: (POcket-CAvity Search Application). an automatic ligand-binding-site prediction program

ProShape: Volume, Surface and Pockets of Proteins

fpocket: pocket detection for protein. Fpocket: perform simple pocket detection. MDpocket: track pockets in molecular dynamics. Hpocket: view conserved pockets withing homologous proteins

GHECOM: A program for finding multi-scale pockets on protein surfaces using mathematical morphology

list of software for pocket finder

list of software for pocket finder ant other structural characteristics

SiteComp: Ligand Binding Site Analisys


Pocket-Finder: pocket detection

Structural Comparison

Strap: intuitive Editor for annotated multiple Sequence and Structure Alignments

ProBis: is a web server and a computer program for the detection of structurally similar protein binding sites and pairwise local structural alignment.

ProSmoS: a pattern-based search using interaction matrix representation of protein structures.

Dali server:The Dali server is a network service for comparing protein structures in 3D

ABS-SCAN In silico Alanine Scanning Mutagenesis for ligand binding site

Electrostatics Potential

PBEQ - solver: provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential

APBS: Adaptive Poisson-Boltzmann Solver

PDB2PQR:This server enables a user to convert PDB files into PQR files.

PDB2PQR:An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations

eF-site: electrostatic surface of functional-site

Delphi:Analytical solutions of the corresponding Poisson-Boltzmann Equation (PBE) are not available for such cases and the distribution of the potential can be found only numerically.

Delphi Online

Structural Characterization

3D-SURFER is web-based software for protein surface comparison and analysis

CASTP:It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecule

Voronoi: Packing Efficiency calculator

SSAP: The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment

Disulfide Bond Analysis tool:Below is our software tool for analyzing disulfide bond

Pro-Origami:The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear. Topology.

HOPE: is an easy-to-use webserver that analyses the structural effects of your mutation of interest. Project HOPE will then collect and combine available information from a series of webservers and databases and will produce a mutation report complete with results.



ASA-view: Solvent Accessibility graphics for proteins

VADAR: (Volume, Area, Dihedral Angle Reporter)

Molecule Builder

COOT: Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data

Arguslab: is a molecular modeling, graphics, and drug design program

Vega zz:

HyperChem:Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods, as well as density functional theory. HyperChem Data and HyperNMR are included as part of HyperChem. New features are continually added and include elegant Open GL rendering, TNDO, RM1, Charmm protein simulations, molecules in magnetic fields, interfaces to third-party applications, calculations of structure, spectra, rate constants and much more. HyperChem is applicable to macromolecules as well as small molecules and is scriptable.

Ascalaph provides the window interface and three-dimensional graphics for molecular modeling. Editing of the molecular geometry and molecular dynamics are also supported.

DNA/RNA building

NAB: Automation of making nucleic acid helices DNA building

3DNA:A Software Package for the Analysis, Rebuilding, and Visualization of Three-dimensional Nucleic Acid Structures.

servers for multiple analysis

Structural Analysis: server of the Ressource Parisienne en Bioinformatique Structurale (RPBS)

other Structural Tools

PDB Cleaner:For manipulations of the pdb file, one can use PDB Cleaner service from IGS-CNRS

Molsurfer Map: The interface between 2 macromolecules (protein/dna/rna) will be mapped by adsi and molecular properties (excluding electrostatics) will be projected onto it.

Surface Area and Solvation Energy of Macromolecules

LIGPLOT: Program for automatically plotting protein-ligand

GRASP: Graphical Representation and Analysis of Structural Properties

Protein side chains relative solvent accessibility prediction

CysState: Cysteines disulfide bonding state prediction from protein sequence

Protein Molecular Weight Calculator

Protein Molecular Weight Calculator

Protein Structure Database Searching by DaliLite v. 3 The Dali server is a network service for comparing protein structures in 3D.

PDB Cleaner:For manipulations of the pdb file, one can use PDB Cleaner service from IGS-CNRS

SDM requires a PDB file of the wild-type protein structure in order to calculate a stability score for mutant proteins.


molecular_mechanics_modeling.txt · Última modificación: 2020/04/14 17:56 por marenas