Databases

PDB database - The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.

CATH - Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

SCOP - Structural Classification of Proteins - database created by a combination of manual inspection and automated methods.

NCBI - site map to extensive services.

Alignment tools

BLAST - Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

ClustalW - aligns multiple sequences

EBI Tools - EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services EBI provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

FASTA Programs - Sequence retrieval and comparison tools.

T-COFFEE - The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool that is more accurate than ClustalW for sequences with less than 30% identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments.

Protein secondary structure prediction

3-D Jury - 3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

PSIPRED - An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.

Protein structure prediction

3-D Jury - 3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

FFAS03 - The Fold & Function Assignment System (FFAS03) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM.

MODELLER - Homology or comparative modeling of 3D protein structures.

to be continued...