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 53 links

Displaying 15 links

3DSSTool Content

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

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.

3MatrixTool Content

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

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

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

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

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

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.

COLORADO-3DTool Content

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

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

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

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.

ElNemoTool Content

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

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.

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