Bioinformatics Links Directory : 3-D Structure Retrieval, ViewingLinks to tools for visualization of 3D structures are found here. This section also contains links to many 3D structure databases.UMMS- (Found July 8, 2008 ) UMass Morph Server (UMMS) is a tool for molecular dynamics simulations that can be used for visualizing and predicting motions of macromolecules such as conformational changes in protein structures.http://biomechanics.ecs.umass.edu/umms.html PDB- (Found July 8, 2008 ) Protein Data Bank; includes theoretical structures.http://www.rcsb.org/pdb/Welcome.do NCBI Structure Group- (Found July 8, 2008 ) Good starting point with links to databases and tools.http://www.ncbi.nlm.nih.gov/Structure/ AISMIG- (Found July 8, 2008 ) AISMIG (An Interactive Server-side Molecule Image Generator) is a tool for generating and visualizing high resolution 3D images from PDB structure files.http://www.dkfz-heidelberg.de/spec/aismig BSDD- (Found July 8, 2008 ) 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.http://iris.physics.iisc.ernet.in/bsdd/ CASTp- (Found July 8, 2008 ) 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.http://sts.bioengr.uic.edu/castp/ CATH- (Found July 8, 2008 ) Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html Cn3D- (Found July 8, 2008 ) Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml ElNemo- (Found July 8, 2008 ) 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.http://igs-server.cnrs-mrs.fr/elnemo/start.html FeatureMap3D- (Found July 8, 2008 ) FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.http://www.cbs.dtu.dk/services/FeatureMap3D/ |