Related Links for PDBSiteScanTool Content

Found 33 links

Displaying 15 links

BSDDDatabase Content

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BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

Catalytic Site IdentificationTool Content

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The Catalytic Site Identification web server provides the ability to find structural matches to a user-specified catalytic site among all Protein Data Bank (PDB) proteins. The web server can also examine a user-specified protein to identify structural matches to a library of catalytic sites.

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CRASPTool Content

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Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.

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.

FunFOLD2Tool Content

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FunFOLD2 is a web server that integrates protein-ligand binding and quality assessment protocols for the prediction of protein function from sequence via structure.

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Institute of Enzymology ServersTool Content

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A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

MatchTool Content

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Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

MATRASTool Content

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MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.

MolProbityTool Content

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MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

MolSurferTool Content

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Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

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