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Links tagged with 'motion'

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ALADYNTool Content

http://aladyn.escience-lab.org [open in a new window]

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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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ALADYN: a web server for aligning proteins by matching their large-scale motion20106
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 [open in a new window]

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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.

links directory index: 293
TitlePublication YearGoogle Scholar Citation Count
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement2004293
NAR Web Server Issue 2004
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tagsmolecular models motion protein conformation proteins x-ray crystallography

ePMVTool Content

http://epmv.scripps.edu/ [open in a new window]

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

We have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (blender,maya and cinema4D) to provide simultaneous access the capabilities of all of the systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease.

This content is being maintained by ludovicautin.

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tags3D algorithms animals blender cinema4d computational biology computer graphics electrocardiography female fetal heart fetal monitoring fetus heart rate humans interdisciplinary communication maya mice modelling molecular biology molecular conformation molecular dynamics simulation molecular graphism molecular models motion movement phtorealistic pregnancy prospective studies rem sleep rendering software three-dimensional imaging user-computer interface vizualisation

MolMovDBDatabase Content

http://molmovdb.org/ [open in a new window]

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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.

links directory index: 136
TitlePublication YearGoogle Scholar Citation Count
MolMovDB: analysis and visualization of conformational change and structural flexibility2003136
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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/ [open in a new window]

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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.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
MovieMaker: a web server for rapid rendering of protein motions and interactions200512
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 [open in a new window]

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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.

This content is being maintained by Marc Delarue.

links directory index: 418
TitlePublication YearGoogle Scholar Citation Count
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis2006114
Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization200543
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models2004102
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model2002159
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 [open in a new window]

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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.

links directory index: 795
TitlePublication YearGoogle Scholar Citation Count
oGNM: online computation of structural dynamics using the Gaussian Network Model200651
iGNM: a database of protein functional motions based on Gaussian Network Model200587
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential1997657
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 [open in a new window]

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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.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity20102
NAR Web Server Issue 2010
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tagschromosome segregation kinetochores microtubules motion

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