Databases and Web Tools

Artificial Intelligence Tools

https://nvidia.github.io/bionemo-framework/ (open sourced BioNeMo)

https://github.com/jwohlwend/boltz (model for biomolecular interaction, newly developed by MIT researchers)

Bacterial

http://metagenomics.anl.gov/ (Huge metagenomics database, great mapping tools)

http://csbl.bmb.uga.edu/DOOR/ (prokaryote operons)

http://bioinfo-mml.sjtu.edu.cn/TADB/ (Toxin-antitoxin pairs)

RNA

http://trnadb.bioinf.uni-leipzig.de/ (tRNA genes)

http://gtrnadb.ucsc.edu/ (organism specific tRNA gene database)

http://www.kazusa.or.jp/codon/ (codon usage and counting tools)

http://www.pseudomonas.com/   (Pseudomonas genome database)

http://tuberculist.epfl.ch/ (TB genes, all)

http://www.tbdb.org/ (TB genes, drug resistance)

http://drnelson.uthsc.edu/Bacteria.html (bacterial cytochrome p450s)

Biochemistry:

http://modomics.genesilico.pl/ (the quintessential RNA modification databse)

http://mods.rna.albany.edu/ (RNA modification database, monooligo calculator is an excellent supplement for oligo mass spectrometry)

http://www.chemspider.com/ (chemical structural database, great for finding vendors too!)

http://www.massbank.jp/?lang=en (mass spectra database, good for MSn studies of small molecules)

http://www.genome.ad.jp/kegg/pathway/map/map00230.html (Purine metabolism interactive database)

Omics:

http://www.genome.jp/kegg/ (the best one-stop shop for integrative pathway analysis)

http://www.uniprot.org/ (proteomics, protein function - consists of Swissprot, which is curated and TremBL which isn't)

http://www.broadinstitute.org/gsea/index.jsp (more of a pipeline than a database, used to look at gene enrichments)

http://david.abcc.ncifcrf.gov/ (functional gene annotations)

http://www.ncbi.nlm.nih.gov/gene (NCBI gene database -- great 1° pass resource)

http://www.ncbi.nlm.nih.gov/geo/ (repository for microarray and RNAseq data - deposition required for submission of RNAseq data)

http://www.ebi.ac.uk/pride/archive/ (proteomics data archive — current MCP submission requirement)

http://www.ebi.ac.uk/GOA (easy-to-use gene ontology resource database)

http://www.ebi.ac.uk/Tools/msa/clustalo/   (multiple sequence alignment program)

Oligos and Molecular Biology:

http://www.snapgene.com/products/snapgene_viewer/ (great tool for molecular cloning)

http://rna.lundberg.gu.se/cutter2/ (analyze restriction map of sequence)

http://www.basic.northwestern.edu/biotools/oligocalc.html

http://www.cellbiol.com/scripts/complement/dna_sequence_reverse_complement.php

http://www.idtdna.com/site (has a webchat system that you can enquire technicalities with their specialist before ordering, especially for long oligos or oligos with modifications etc) 

http://web.expasy.org/translate/ 

http://www.biomol.net/en/tools/proteinextinction.htm

http://www.restrictionmapper.org/

http://tools.neb.com/NEBcutter2/index.php

http://research.med.helsinki.fi/plasmadna/Download/Mac_Version.htm (good for drawing constructs, free version for mac and windows) 

Web Sites of Our Collaborators

Prof. Sylvie Alonso, National University of Singapore

Prof. Tom Begley, University of Albany

Prof. Thomas Dick, National University of Singapore

Prof. Julien Lescar, Nanyang Technological University

Prof. Liu Chuan Fa, Nanyang Technological University

Prof. Mu Yuguang, Nanyang Technological University

Prof. Kevin Pethe, Lee Kong Chian School of Medicine, Nanyang Technological University

Prof. Peter Preiser, Nanyang Technological University

Dr. Pei-yong Shi, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston

Prof. James Tam, Nanyang Technological University

MIT Chemical Hygiene

MIT EHS training site (http://mitehs.traincaster.com/)

Biological Engineering Division Safety Web Pages (all new lab members must go here: http://web.mit.edu/be/resources/index.htm)