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Links tagged with 'static electricity'

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ClusProTool Content

http://cluspro.bu.edu/login.php

Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

NAR Web Server Issue 2007
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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

FastContactTool Content

http://structure.pitt.edu/servers/fastcontact/

Protein > Molecular Dynamics and Docking

FastContact is a free energy scoring tool for protein-protein complex structures.

NAR Web Server Issue 2007
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tagsalgorithms amino acids binding sites biological models chemical models computational biology computer simulation hydrogen bonding molecular models protein binding protein conformation protein interaction mapping protein sequence analysis proteins solvents static electricity thermodynamics

GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/

Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.

This content is being maintained by alexkant.

NAR Web Server Issue 2011
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tagsalgorithms fourier analysis multiprotein complexes mutagenesis protein interaction mapping protons static electricity

MolSurferTool Content

http://projects.villa-bosch.de/dbase/molsurfer/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

NAR Web Server Issue 2003
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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

PBEQ-SolverTool Content

http://www.charmm-gui.org/?doc=input/pbeqsolver

Protein > Biochemical Features

PBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential.

NAR Web Server Issue 2008
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tagscell membrane dna mathematical computing molecular models protein databases proteins rna static electricity

PCETool Content

http://bioserv.rpbs.jussieu.fr/Help/PCE.html

Protein > Biochemical Features

PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.

NAR Web Server Issue 2005
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tagshydrogen-ion concentration molecular models muramidase proteins static electricity

PDB2PQR ServerTool Content

http://pdb2pqr.sourceforge.net/

Protein > 3-D Structural Features
Protein > Biochemical Features

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.

NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

NAR Web Server Issue 2006
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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

PFPTool Content

http://pfp.technion.ac.il/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PHEMTOTool Content

http://phemto.orgchm.bas.bg/

Protein > 3-D Structural Features
Protein > Biochemical Features

Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics.

NAR Web Server Issue 2009
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tagsalgorithms hydrogen-ion concentration proteins static electricity

PHEPSTool Content

http://pheps.orgchm.bas.bg/home.html

Protein > 3-D Structural Features
Protein > Biochemical Features

pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.

NAR Web Server Issue 2006
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tagshydrogen-ion concentration ions proteins protons static electricity

PreBITool Content

http://pre-s.protein.osaka-u.ac.jp/prebi/

Protein > 3-D Structural Features

Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.

NAR Web Server Issue 2006
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tagsdatabase management systems humans hydrophobic and hydrophilic interactions molecular models multiprotein complexes protein conformation protein databases proteins static electricity three-dimensional imaging x-ray crystallography

R.E.D.Tool Content

http://q4md-forcefieldtools.org/REDS/

Protein > 3-D Structure Prediction

R.E.D. Server is designed to build force field libraries for new molecules and molecular fragments. One can derive molecular electrostatic potential-based atomic charges embedded in force field libraries for use in force field development, charge validation and molecular dynamics simulations.

NAR Web Server Issue 2011
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tagscalixarenes molecular dynamics simulation quantum theory static electricity

webPIPSATool Content

http://pipsa.h-its.org

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.

This content is being maintained by wade.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological models chemical models computer simulation electrostatics enzyme activation enzymes kinetics protein binding protein conformation protein interaction mapping proteins research signal transduction static electricity systems biology triose-phosphate isomerase