3-D Structure Prediction

This section contains links to resources to aid in protein 3D structure prediction.

Found 110 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

@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.

AIDATool Content

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AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation producing a final assembly satisfying user-specified inter-domain distance restraints.

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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

BeEPTool Content

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The BeEP (Best Evolutionary Pattern) web server is an online resource to help in protein structure prediction. It ranks submitted structural models of a protein using evolutionary information.

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Berkeley Phylogenomics GroupTool Content

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The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

This content is being maintained by kimmen.

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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CABS-flexTool Content

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CABS-flex web server implements CABS-model based protocol for the fast simulations of protein structure fluctuations.. Input is a PDB file.

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