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Links tagged with 'motion'

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ALADYNTool Content

http://aladyn.escience-lab.org

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

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.

NAR Web Server Issue 2010
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tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

NAR Web Server Issue 2004
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tagsmolecular models motion protein conformation proteins x-ray crystallography

MolMovDBDatabase Content

http://molmovdb.org/

Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.

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tagsdata collection genetic databases molecular models motion nucleic acid conformation protein conformation rna

MovieMakerTool Content

http://wishart.biology.ualberta.ca/moviemaker/

Protein > 3-D Structure Retrieval/Viewing

MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions.

NAR Web Server Issue 2005
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tagsligands motion motion pictures as topic myoglobin protein folding proteins rotation vibration

NOMAD-RefTool Content

http://lorentz.immstr.pasteur.fr/nomad-ref.php

Protein > Molecular Dynamics and Docking

Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.

NAR Web Server Issue 2006
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tagscarrier proteins computer simulation dna dna-binding proteins dna-directed dna polymerase dna-directed rna polymerases escherichia coli proteins ligands macromolecular substances mathematical computing molecular models molecular structure motion neural networks (computer) protein conformation proteins x-ray diffraction

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm

Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

ParticleStatsTool Content

http://www.ParticleStats.com

Protein > Molecular Dynamics and Docking

ParticleStats is a web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects.

This content is being maintained by rshamilton.

NAR Web Server Issue 2010
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tagschromosome segregation kinetochores microtubules motion

PMGTool Content

http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG

Protein > 3-D Structure Retrieval/Viewing

The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.

This content is being maintained by ludovicautin.

NAR Web Server Issue 2007
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tagscomputational biology computer simulation ligands motion motion pictures as topic programming languages protein folding proteins rotation time factors vibration