3-D Structure Comparison

Resources for the comparison of sequences at the level of tertiary structure are also found here. This includes tools for superimposing structures and for creating structural alignments.

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Displaying 15 links

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

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.

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

@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.

AH-DBDatabase Content

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Database of protein structure pairs (apo-holo structure pairs) before and after binding. AH-DB is designed to provide an easy and unified way to prepare apo-holo structure pair data for studies. Data is generated by identifying/mapping molecules in Protein Data Bank (PDB) entries.

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ALADYNTool Content

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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.

ASSAMTool Content

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ASSAM tool searches for patterns of amino acid side chains in 3D space within PDB structures. Input must be a 3D amino acid pattern, which will be used in based on distances between the amino acid side chains.

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CAD-scoreTool Content

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The CAD-score web server provides a contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

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CHC_FINDTool Content

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CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

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