Links
Software
ICMLite:
A stand alone viewer and computational biology program which has superb OpenGL based graphics which perform the usual functions of
displaying a model in solid ribbon, wire, ball, stick, xstick, cpk, and dot surface. ICMLite is available on a variety of platforms.
ICMLite also includes many things not offered by most other programs, such as manual docking, interactive model building, perspective,
interactive zoom, independent clipping planes, eight switchable and combinable image buffers, flexible secondary structure assignment,
chemical bonds or topological trees, image annotation, multiple object loading and display, and selection of atom/residue/molecules
by types and patterns. ICMLite also can be used in either command line form or gui.
Rasmol:
A molecular viewer for Windows, Linux and other OSs.
Database retrieval and Servers
Roland Dunbrack's culled PDB lists:
Lists of PDB chains that conform to user-defined criteria:
- maximum mutual sequence identity
- minimum and maximum resolution
- minimum and maximum chain length
- maximum R-values
- include or don't include NMR chains
- include or don't include CA-only entries
Sequence identities for each pair of proteins is determined from Gapped-BLAST results of an all-against-all comparison of the PDB.
If two sequences share a segment of 40 amino acids or more with sequence identity over the cutoff, then only one of them will be
retained in the culled list. The lists are optimized to provide chains with the highest resolution available among similar or
identical sequences.
Homology modelling tool MODELLER Fugue is a threading server that will also yield threaded PDB files as output:
http://www-cryst.bioc.cam.ac.uk/~fugue/.
MultiProt (for structural alignment) and STACCATO (for structure based sequence alignment). STACCATO accepts both structures and sequences
without structures. The output is in ClustalW format.
http://bioinfo3d.cs.tau.ac.il/MultiProt/
http://bioinfo3d.cs.tau.ac.il/staccato/
Structure-based sequence alignment with T-Coffee, either via the following web-server
http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi
or as stand-alone version:
http://www.igs.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
Software that can take omega, phi and psi dihedrals and generate three-dimensional coordinates of a peptide: The "protein" program within
the Tinker package can do this. You just need create an input file with lines that look like: resname phi psi omega chi1 chi2
chi3 chi4
(where resname can be 1 or 3 letter code and omega chi1 chi2 chi3 chi4 are optional).
Tinker is available from http://dasher.wustl.edu/tinker/.
RESP ESP charge DDataBase
http://www.u-picardie.fr/labo/lbpd/REDDB/ for molecular mechanics and docking studies, and use in force field based simulations.
Identifciation of supersecondary structures (such as beta-hairpins, beta-alpha-beta motifs etc.) in a PDB file.
'Small Hydrogen-Bonded Motifs' database at:
http://doolittle.ibls.gla.ac.uk:9006/david/ProteinMotifDB.html.
http://www.ebi.ac.uk/msd-srv/msdmotif/
Gene3D:
http://bsmmac1.biochem.ucl.ac.uk:8080/Gene3D/ includes its annotations as well as the EBI-MSD database,
http://www.ebi.ac.uk/msd/.