Bioinformatics

Sequence only

• Servers and programs for sequence analysis

Sequence to structure

• Prediction of structure from sequence: servers and programs
• Mapping sequence alignment to a structure

Structure to Sequence

• Structure based sequence alignment

Structure only

• Servers for ligand topologies/parameters
• Servers and programs for protein structure analysis
• Programs for nucleic acid structure analysis
• Morphing
• Programs for representing the surface of a channel inside protein
• database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam
• Rosetta Alanine Scanning each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated
• [1] offering an interface for comparing a number of different methods for automatic domain definition

Functional annotation

• GOdot webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105)
• ProFunc Analysis of a protein's 3D structure to help identify its likely biochemical function
• Annotation PSI Stuctural Genomics knowledgebase

Docking

• ClusPro - easy to use web interface
• Rosetta can do much more than just docking, but is difficult to use
• 3D-dock - uses an algorithm that mainly looks at surface complimentarity between the two proteins
• Dave Ritchie's Hex program - it is blisteringly quick
• Haddock - recommended by Tassos
• AutoDock - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock
• DockBlaster - runs DOCK 3.5.54; there's a wiki

Other stuff

• Programs for visualization (see also Model building)

• Links to Bioinformatics websites

• programs with chemistry knowledge, e.g. to build 3D-coordinates from 2D drawings