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Biochemistry and Molecular Biology Subject Guide: More Resources

Going Beyond Google

Websites

YeastBook
A comprehensive compendium of reviews that presents the current state of knowledge of the molecular biology, cellular biology, and genetics of S. cerevisiae.

Search Engines

Google Scholar
The Google Scholar search engine locates scholarly literature from a wide variety of academic publishers, professional societies, preprint repositories and universities, as well as scholarly articles available across the web. Results are ranked by relevance, taking into account the full text of each article as well as the article’s author, the publication in which the article appeared and how often it has been cited in scholarly literature. Search results may include citations of older works and seminal articles that appear only in books or other offline publications.
Science.gov
This search engine searches more than 36 databases and 1850 selected web sites with 200 million pages of U.S. government science information

Gateways

ExPASy Life Science Directory
Formerly known as Amos’ WWW Links, this list contains almost exclusively pointers to information sources for life scientists with an interest in biological macromolecules. The list is organized by category.

Open Access Databases

ENZYME
The SWISS-PROT Enzyme Nomenclature database is a repository of information relative to the nomenclature of enzymes. It describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. Access by EC number, enzyme class, official or alternative name(s), chemical compound, cofactor or by search in common lines.
RCSB Protein Data Bank
The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. The site provides links to many relevant resources including databases, sequence analysis tools, structure classification and analysis, and more.
RefSeq
The Reference Sequence (RefSeq) collection is a curated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. A representative GenBank record is used as the source for a RefSeq record with additional relevant information added by experts. There is one record for each gene, or each splice variant, from each organism represented. Each record is intended to present an encapsulation of the current understanding of a gene or protein. RefSeq is accessible through Entrez, LocusLink and BLAST.
Swiss-Prot
Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Related databases and tools are available at the ExPASy, (Expert Protein Analysis System) from the Swiss Institute of Bioinformatics (SIB).

Tools

BLAST (Basic Local Alignment Search Tool)
BLAST is a program that finds areas of similarity in nucleotide and protein sequences. In addition to the application, there is a good web based version.
Cn3D
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service. Cn3D runs on Windows, Macintosh and Unix. Cn3D simultaneously displays structure, sequence and alignment, and now has powerful annotation and alignment editing features.
NCBI Genome Data Viewer
The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of annotated eukaryotic genome assemblies. The GDV browser can visualize different types of molecular data in a whole genome context, including gene annotation, BLAST alignments, and experimental study data from the NCBI GEO and dbGaP databases. GDV release notes describe new features relating to this browser.
PyMOL
PyMOL is a widely used open-source molecular visualization system.
 

Interim Librarian

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Zach Sharrow
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