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.

Found 61 links

Displaying 15 links

3DEM LoupeTool Content

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3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies.

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3DLigandSiteTool Content

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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.

3DTFTool Content

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3D Transcription Factor (3DTF) is a web-server for the analysis of protein-DNA binding sites. It calculates the positional weight matrix (PWM), representing the DNA-binding specifity of the protein.

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@TOME-2Tool Content

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@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.

BeAtMuSiCTool Content

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BeAtMuSiC is a coarse-grained predictor of the changes in binding free energy induced by point mutations, using the structure of the protein-protein complex as input.

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Bioinformatics ToolkitTool Content

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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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CovalentDock CloudTool Content

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CovalentDock Cloud web server allows one to perform covalent docking experiments and analysis online. Input is the structure of both the ligand and the receptor.

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DEPTHTool Content

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

ElNemoTool Content

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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.

EpiToolKitTool Content

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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.

ePMVTool Content

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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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