> > Molecular Dynamics and Docking

Molecular Dynamics and Docking

This section includes resources for molecular dynamics including tools that can predict the movements of structures and/or conformational changes. Molecular docking servers are also included here.

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Found 44 links

Displaying 15 links

3DLigandSiteTool Content

http://www.sbg.bio.ic.ac.uk/3dligandsite

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Molecular Dynamics and Docking

3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.

NAR Web Server Issue 2010
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tagsalgorithms binding sites ligands molecular models protein sequence analysis protein structural homology reproducibility of results

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

NAR Web Server Issue 2004
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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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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

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth

Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

NAR Web Server Issue 2011
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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

EpiToolKitTool Content

http://www.epitoolkit.org

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Molecular Dynamics and Docking

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

NAR Web Server Issue 2008
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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

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

FiberDockTool Content

http://bioinfo3d.cs.tau.ac.il/FiberDock/

Protein > Molecular Dynamics and Docking

FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.

NAR Web Server Issue 2010
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tagsalgorithms molecular models multiprotein complexes protein conformation protein interaction mapping

FireDockTool Content

http://bioinfo3d.cs.tau.ac.il/FireDock/

Protein > Molecular Dynamics and Docking

The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.

NAR Web Server Issue 2008
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tagsalgorithms molecular models multiprotein complexes protein interaction mapping

FOLD-RATETool Content

http://psfs.cbrc.jp/fold-rate/

Protein > Molecular Dynamics and Docking

FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acids binding sites chemical models kinetics linear models molecular models mutation protein conformation protein folding protein sequence analysis protein structural homology proteins secondary protein structure solvents statistical models statistics as topic tertiary protein structure thermodynamics

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

NAR Web Server Issue 2005
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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

Tags associated with subcategory 'Protein/Molecular Dynamics and Docking'

protein conformation molecular models proteins algorithms ligands binding sites computational biology protein interaction mapping computer simulation protein sequence analysis tertiary protein structure multiprotein complexes humans thermodynamics chemical models protein databases protein folding protein structural homology macromolecular substances actins ribosomal rna rna mathematics motion adenosine triphosphate lactoferrin dna-directed rna polymerases elasticity dna polymerase beta dictyostelium animals biophysical phenomena biophysics l-lactate dehydrogenase x-ray diffraction solvents statistics as topic dna-directed dna polymerase molecular structure kinetics neural networks (computer) linear models capsid carbon cryoelectron microscopy ions escherichia coli proteins citrate (si)-synthase chaperonin 10 chaperonin 60 mathematical computing protein binding kinesin capsid proteins exotoxins bacterial proteins antigen receptors entropy pharmaceutical preparations antibodies influenza virus hemagglutinin glycoproteins membrane proteins single nucleotide polymorphism protein engineering x-ray crystallography nucleic acid conformation mutation phosphoenolpyruvate sugar phosphotransferase system protein-serine-threonine kinases viral antigens drug design dna principal component analysis secondary protein structure nucleotides myosins mice molecular conformation molecular motor proteins proton-translocating atpases protozoan proteins hydrogen bonding tamoxifen vitamin e viral proteins theoretical models statistical models structure-activity relationship taq polymerase dna-binding proteins sequence alignment hormones alpha-amylases artificial intelligence cytoplasmic and nuclear receptors bacteriophages child triose-phosphate isomerase antigen-antibody complex automation point mutation