Links tagged with 'molecular models'

Found 176 links

Displaying 15 links

(PS)2 Protein Structure Prediction ServerTool Content

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(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
(PS)2: protein structure prediction server200627

3D-FunTool Content

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3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
3D-Fun: predicting enzyme function from structure20086

3didDatabase Content

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The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

3DSSTool Content

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3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
3dSS: 3D structural superposition200632

3MatrixTool Content

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3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

@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.

AquaSAXSTool Content

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AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.

This content is being maintained by Marc Delarue.

ArchPredTool Content

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ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
ArchPRED: a template based loop structure prediction server200626

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