3-D Structure Retrieval/Viewing

Links to tools for visualization of 3D structures are found here. This section also contains links to many 3D structure databases.

Found 67 links

Displaying 15 links

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.

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.

CD-SearchDatabase Content

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CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.

This content is being maintained by Aron Marchler-Bauer.

Cell++Tool Content

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Cell++ is a novel stochastic simulation environment which is capable of modelling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signalling.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
Cell++--simulating biochemical pathways200619

Cn3DTool Content

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Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.

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external linksLink on Wikipedia

CognoscenteDatabase Content

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Cognoscente is a database and visualization tool for biomolecular interactions that have been documented in the literature. Entrez Gene Symbols or Entrez Gene ID numbers may be used to form a query, and a lookup tool is provided to help you identify the appropriate symbols or IDs to use for your gene of interest.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

COLORADO-3DTool Content

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COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.

COPSTool Content

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The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
COPS--a novel workbench for explorations in fold space200914

Crystallography Open DatabaseResource Content

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Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known 'small molecule / small to medium sized unit cell' crystal structures and makes them available freely on the Internet.

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