International Nucleotide Sequence Database Collaboration

• NCBI - National Center for Biotechnology Information (GenBank database)
• EBI - European Bioinformatics Institute (EMBL database and other stuff)
• DDBJ - DNA Data Bank of Japan
• Feature Table Definition - the format of entries in these databases

Protein Sequence Databases

• SWISS-PROT & TrEMBL - annotated protein sequence database and computer annotated supplement
• PIR - Protein Information Resource
• MIPS - Munich Information centre for Protein Sequences

Sequence Similarity Search

• BLAST @ NCBI
• PSI-BLAST @ NCBI
• FASTA @ EBI
• ParAlign / Smith-Waterman Search

Sequence Alignment

• ClustalW @ EBI - multiple sequence alignment
• Spidey - an mRNA-to-genomic alignment program
• SIM4 - a program to align cDNA and genomic DNA
• BAliBASE - a benchmark alignments database for the evaluation of multiple sequence alignment programs
• WebLogo - a web based sequence logo generator
• Whole Genome Human/Mouse Alignments

Protein 3D Structure Resources

• PDB - protein 3D structure database
• RasMol / Protein Explorer - molecule 3D structure viewers
• VMD - another 3D structure viewer from UIUC
• SCOP - Structural Classification Of Proteins
• UCL BSM CATH classification
• The DALI Domain Database
• SWISS-MODEL - homology modeling server
• DALI - 3D structure alignment server

Journals

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• Medline / PubMed
• NEC Research Index
• UIC Library Electronic Journals
• Advances in Neural Information Processing Systems
• Bioinformatics
• BMC Bioinformatics
• Current Opinion of Structural Biology
• Genome Biology
• Genome Informatics Journal (Proceedings of Genome Informatics Workshop)
• Genome Research
• Immunome Research
• Journal of Chemical Information and Computer Science
• Journal of Computational Biology
• Journal of Molecular Biology
• Machine Learning
• Nature
• Nature Genetics
• PLoS Computational Biology
• Proceedings of Annual Conference on Research in Computational Molecular Biology (RECOMB)
• Proceedings of the National Academy of Sciences of the United States (PNAS)
• Proceedings of Pacific Symposium on Biocomputing
• Proteins
• Protein Engineering
• Protein Science
• Science
• Trends in Biochemical Sciences