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Links tagged with 'molecular dynamics simulation'

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BSDBDatabase Content

http://www.ifpan.edu.pl/BSDB/

Protein > Databases

The Biomolecule Stretching Data provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. Information on the possible types of the mechanical clamps (the motifs which are responsible for a protein's resistance to stretching) are also given.

NAR Database Issue 2011
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tagsbiomechanics chemical models molecular dynamics simulation protein databases proteins secondary protein structure

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

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Other Molecules > Small Molecules
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

NAR Web Server Issue 2010
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tagsbinding sites hemoglobins ligands molecular dynamics simulation protein conformation protein structural homology

POLYVIEW-MMTool Content

http://polyview.cchmc.org/conform.html

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization.

NAR Web Server Issue 2010
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tagsalgorithms capsid proteins documentation molecular dynamics simulation molecular models peptides protein conformation protein databases protein interaction mapping protein sequence analysis proteins tertiary protein structure

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

SMOG@ctbpTool Content

http://smog.ucsd.edu

Protein > 3-D Structure Prediction

SMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials.

This content is being maintained by smogatctbp.

NAR Web Server Issue 2010
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tagsdna molecular dynamics simulation protein folding proteins rna