Research Guides: CHEM 360: Biochemistry (Bencze): STEP 3: Proteins &amp; Genes

Protein and Gene Databases

STEP 3: Protein and Gene Information

Use the links below to locate protein and genetic information about the medical condition. Start by typing your medical condition (or the protein you've identified in your background research that's linked to your medical condition) and make sure that the protein you select is for humans or homo sapiens instead of another species.

Protein Data Bank
Provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). Once you locate the protein detail page, you'll see related literature. Click on the "3D View" tab to see the genomic sequence and a model. Click on the "Sequence" and "Genome" tab to learn more about its location.
OMIM (Online Mendelian Inheritance in Man)
An online catalog of human genes and genetic disorders. Search your medical condition (or known protein). The left side of a protein page has a table of contents and features headings of major findings and references in the literature. The right side contains external links for more information. Be sure to note the * ##### near the top of the page to come back to it.

PubMed Central This link opens in a new window
Use the dropdown menu to find protein and gene information. Select "Protein" and search. Then select "Nucleotide" and search again to find the genomic sequence.

Sequence Analysis

Sequence Analysis Databases

ExPASy Bioinformatics Resource Portal
Provides access to over 160 databases and software tools, developed by Swiss Institute of Bioinformatics Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.
ExPASy ProtParam
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 (GRAVY)

Sequence Similarity

BLAST (Basic Local Alignment Search Tool)
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. Use for sequence similarity.

Multiple Sequence Alignment

Clustal Omega
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. For multiple sequence alignment.
UniProt
Provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. For multiple sequence alignment.

Visualization Software for Proteins/Molecules

Protein Structure Visualization Software

PyMOL
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
RasMol
RasMol is a program for molecular graphics visualization to view macromolecules and to prepare publication-quality images.

Next Steps

What's Next?

Continue to fill in the gaps of your research by using other databases during:

STEP 4: Scholarly Literature

CHEM 360: Biochemistry (Bencze)

Interlibrary Loan

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