Bioinformatics links and tools
NCBI's tools http://www.ncbi.nlm.nih.gov/Tools/
EBI tools http://www.ebi.ac.uk/Tools/
Expasy tools http://ca.expasy.org/
Molecular Station http://www.molecularstation.com/
The Virtual Library of Biochemistry, Molecular Biology and Cell Biology http://www.biochemweb.org/
Multiple Sequence Alignment Tools
A collection of MSA software http://en.wikipedia.org/wiki/List_of_sequence_alignment_software
MAFFT http://mafft.cbrc.jp/alignment/software/
Protein analysis and structural predictions
A collection of software http://en.wikipedia.org/wiki/Protein_structure_prediction
Swiss-Model http://swissmodel.expasy.org/
PHYRE http://www.sbg.bio.ic.ac.uk/~phyre/
iTasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Pairwise structural comparison at EBI (Dali Lite) http://www.ebi.ac.uk/Tools/dalilite/index.html
Pairwise structural comparison at CATH (SSAP) http://www.cathdb.info/cgi-bin/SsapServer.pl
Visualization of elctrostatic potential http://www.charmm-gui.org/?doc=input/pbeqsolver
more coming soon