Science Links

RCSB Protein Data Bank: This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

ExPASy SIB Bioinformatics Resource Portal:Provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

PubMed: PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

OriginLab: A scientific graphing and data analysis software.

PyMOL: A user-sponsored molecular visualization system on an open-source foundation.

Jmol: An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.

UniProt: Sequence alignment program.

Clustal Omega: A new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.

Blast: The 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.

ProtParam: A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered protein sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.

PeptideCutter: Predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and /or a table of cleavage site positions.

Compute pI/Mw tool: A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences.

Promethease: Promethease is a literature retrieval system that builds a personal DNA report based on connecting a file of DNA genotypes to the scientific findings cited in SNPedia. This is a great way to get similar health info like 23andme without the cost.