LibGuides: Biochemistry Research Guide: Internet Resources

Internet Sites

Wikipedia - Portal: Science
Proteopedia
The free, collaborative 3D-encyclopedia of proteins & other molecules
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. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
Pfam
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
ExPASy: SIB Bioinformatics Resource Portal
ExPASy is the SIB Bioinformatics Resource Portal which 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.
UniProtKB/Swiss-Prot
UniProtKB/Swiss-Prot is the expertly curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.
ProtParam - Protein Parameters
Also: http://protparam.net/index.html Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
NCBI BLAST
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
PyMOL
A molecular visualization system on an open source foundation, maintained and distributed by Schrödinger
BRENDA: The comprehensive enzyme information system
BRENDA is the main collection of enzyme functional data available to the scientific community. It is available free of charge via the internet (www.brenda-enzymes.org) and as an in-house database for commercial users (requests to our distributor geneXplain).
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BRENDA is maintained and developed at the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig, Germany. Data on enzyme function are extracted directly from the primary literature by scientists holding a degree in Biology or Chemistry. Formal and consistency checks are done by computer programs, each data set on a classified enzyme is checked manually by at least one biologist and one chemist.
Europe PMC
Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. Europe PMC provides links to relevant records in databases such as Uniprot, European Nucleotide Archive (ENA), Protein Data Bank Europe (PDBE) and BioStudies.
WikiGenes
WikiGenes is a non-profit initiative to provide a global collaborative knowledge base for the life sciences, where authorship matters.
Global Science Gateway
This website is a single launch point for searching multiple national and international sites in a variety of languages.
Toxnet
From the National Institutes of Health, this database is a free government resource that gives details on a wide variety of toxic and hazardous chemicals.
Scitable Blogs
By Nature Publishing Group. Focuses on cell biology, including the topics of evolution, gene expression, and the rich complexity of cellular processes shared by living organisms. Scitable also offers resources for the student scientist, with advice about effective science communication and career paths.
E-Print Network
E-Print Network a gateway to over 35,300 websites and databases worldwide, containing over 5.5 million e-prints in basic and applied sciences, primarily in physics but also including subject areas such as chemistry, biology and life sciences, materials science, nuclear sciences and engineering, energy research, computer and information technologies, and other disciplines of interest to DOE.
Plants Database
The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. Hosted by the USDA.