Resources

Useful Scientific resources

Bioinformatics software/database

1. antiSMASH: antibiotics & secondary metabolite analysis shell.

2. RODEO: algorithm for the analysis of biosynthetic gene clusters, with an emphasis on RiPPs .

3. BLAST: finds regions of similarity between biological sequences.

4. Consurf: identifies conserved residues in homologous proteins.

5. EFI-Enzyme Similarity Tool: tool for generation of sequence similarity networks.

6. HHPred: secondary structure homology prediction.

7. Integrated Microbial Genomics (IMG): analysis, annotation, and distrubtion of microbial genome datasets.

8. InterPro: functional analysis of proteins by classification into familes, predicting domains and important sites.

9. UniProt: a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

10. Clustal Omega: multiple sequence alignment program.

11. MUSCLE: multiple sequence alignment creation.

12. PRISM: bioinformatic tool for the identification of unknown, genetically encoded natural products found within an input sequence.

13. PyMOL: 3D Molecular Visualization.

14. Protein Data Bank: repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.

15. Skylign: logo creation.

16. NEB Tools and Resources: interactive tools from NEB for research and experimental design.

17. Expasy-Translate: translation of a nucleotide sequence to a protein sequence.

18. Expasy-ProtParam: computation of various physical and chemical parameters for a given protein.

19. PeptideCutter - Expasy: predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.

20. PeptideMass - Expasy: computes the masses of the generated peptides.

21. IDT OligoAnalyzer: calculates properties of oligonucleotides.

22. RadicalSAM.org: RadicalSAM.org enables the use of the EFI's genomic enzymology web tools for studies of the radical SAM superfamily.

23. MIBiG: database of biosynthetic gene clusters.

24. KEGG: Kyoto Encyclopedia of Genes and Genomes: database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

25. BRENDA : The Comprehensive Enzyme Information System.

26. STRING: database of known and predicted protein interactions.

Microbiology Culture Collection

1. ATCC

2. DSMZ

3. NCCS

4. NRRL Culture Collection:USDA ARS

5. NCIM

6. MTCC

Chemistry software/database

1. Chemcalc Molecular Formula Finder: generate a list of molecular formulas from an accurate mass.

2. Dinesh NMR: peptide NMR tools, including Random coil Proton Chemical shifts.

3. GNPS: Global Natural Products Social Molecular Networking: mass spectra datasets and network analysis.

4. ProteinProspector: proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.

5. RESID Database: database of known protein modifications.

6. Current Antibiotic Pipeline: the current list of antibiotics undergoing clinical trials.

7. Dictionary of Natural Products: structure and biological origin of natural products.

8. PubChem: information on the biological activities of small molecules.

9. PubMed: free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics.

10. SciFinder: CAS database of chemical and bibliographic information.