General

PDB (Protein Data Bank)

National Center for Biotechnology Information

ExPASY Molecular Biology Server

EBI (European Bioinformatics Institute) Toolbox

DeepView site

DeepView tutorial

IUPAC naming conventions

Molecular evolution glossary

        Genomes

TIGR comprehensive microbial resource

        Miscellaneous

NCBI ORF Finder

        Sequence Similarity Searching by Pairwise Local Alignment

NCBI BLAST server (including PSI-BLAST)

FASTA and SSEARCH (Smith-Waterman)

        Sequence Similarity Searching Using HMMs, PSSMs

SAM-T02 HMM server

PSI-BLAST (see above)

MEME/MAST/Meta-MEME (find sequence motifs, represent them as HMMs, do searches with them)

        Searchable Domain Profile and Sequence Motif Databases

SMART

Pfam (St. Louis)

IMPALA program for searching BLOCKS database

RPS-BLAST (Reverse position-specific BLAST): see NCBI BLAST server

PROSITE

        Structure Prediction Servers

Robetta Server

Jpred (consensus secondary structure prediction)

PredictProtein server

3D-PSSM Fold Recognition server

HMMSTR/iSites/Rosetta

        Major Structural Classification/Alignment Websites

SCOP

CATH

DALI/FSSP

        Multiple Sequence Alignment Programs

CLUSTALW (software also downloadable)