> > 3-D Structure Retrieval/Viewing

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.

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Found 53 links

Displaying 15 links

3DSSTool Content

http://cluster.physics.iisc.ernet.in/3dss/options.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

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.

NAR Web Server Issue 2006
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tagsmolecular models phospholipases a protein databases protein structural homology water

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

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.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

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.

NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

CATHDatabase Content

http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

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tagsamino acid sequence homology animals automation genomics protein databases protein folding protein structural homology proteins secondary protein structure tertiary protein structure

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

CD-SearchDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

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.

NAR Web Server Issue 2004
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tagsamino acid sequence animals consensus sequence conserved sequence molecular models protein databases protein sequence analysis proteins sequence alignment tertiary protein structure time factors

Cn3DTool Content

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Protein > 3-D Structure Retrieval/Viewing

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

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tagsamino acid sequence amino acid sequence homology chemical models computer simulation factual databases molecular sequence data national institutes of health (u.s.) protein conformation proteins tertiary protein structure united states

COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing

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.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence color conserved sequence molecular models protein conformation protein structural homology

COPSTool Content

http://cops.services.came.sbg.ac.at/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

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.

NAR Web Server Issue 2009
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tagsmolecular models protein databases protein folding proteins tertiary protein structure

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

NAR Web Server Issue 2004
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tagsmolecular models motion protein conformation proteins x-ray crystallography

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

Tags associated with subcategory 'Protein/3-D Structure Retrieval/Viewing'

proteins molecular models protein databases protein conformation amino acid sequence sequence alignment tertiary protein structure animals protein sequence analysis protein structural homology molecular sequence data computational biology amino acid sequence homology algorithms computer simulation factual databases conserved sequence amino acid motifs humans viral proteins database management systems ribosomal rna statistical models theoretical models dna-binding proteins molecular conformation motion pictures as topic protein folding motion systems integration transcription factors mutation rhodopsin macromolecular substances mathematics chaperonin 60 citrate (si)-synthase chaperonin 10 carbon zinc fingers biophysics capsid cryoelectron microscopy streptococcus pneumoniae src homology domains biophysical phenomena lactoferrin l-lactate dehydrogenase elasticity rotation ions fungal proteins vibration single nucleotide polymorphism hydrogen bonding ribonucleases peptides rna structure validation three-dimensional imaging secondary protein structure molecular structure automation reproducibility of results time factors sequence homology genetic databases nucleic acids sequence analysis protein nucleic acid conformation molecular evolution phylogeny rna-binding proteins false positive reactions binding sites chemical models cytochrome p-450 enzyme system protein binding proteomics myoglobin x-ray crystallography molecular graphics mathematical computing proprotein convertases saccharomyces cerevisiae succinate dehydrogenase software design quaternary protein structure rats arabidopsis autoimmune diseases azurin genomics acquired immunodeficiency syndrome genome europe European Bioinformatics Institute (EBI) bacterial genome computer-assisted numerical analysis hiv