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Information resources on the chemistry and biochemistry of proteins: lecture notes, databases, journals, research etc.

Online available information resources on the biochemistry of proteins.

Further information categories about related topics are listed in the navigation menu on the left side of these page.

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Current Stories and Reports

New Technique Takes Snapshots of Proteins as They Fold
Scientists have invented a way to 'watch' proteins fold - in less than thousandths of a second - into the elaborate twisted shapes that determine their function - [e]

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General Information

Membrane Proteins of Known Three-Dimensional Structure
from the Stephen White laboratory at UC Irvine - [e]

Principles of Protein Structure, Comparative Protein Modelling and Visualisation
Introduction to Protein structure. Online course - [e]

Protein Kinase Resource, PKR
... is a web accessible compendium of information on the protein kinase family of enzymes - [e]

Protein Structure and Function
An overview - [e]

PSA Protein Structure Prediction Server
The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence. BMERC, USA - [e]

Wnt proteins
Genes, Proteins, Methods, Pathways. Stanford University, USA - [e]

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Lecture Notes, Tutorials

Gel Filtration
Principles and methods. Amersham - Format: PDF - [e]

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Data and Databases

3-D Protein Structure
Databases and Tools for 3-D Protein Structure Comparison and Alignment (USA) [e] - [e]

Aminoacyl-tRNA Synthetase Database. A hypertext version of the database published in the 2000 Database Issue of the Nucleic Acids Research - [e]

Archaeal and Bacterial ABC transporter database - [e]

ASPD (Artificial Selected Proteins/Peptides Database) is a curated database on selected from randomized pools proteins and peptides. Database access is realised by means of simple search system and SRS (Sequence Retrieval System). ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, ...) - [e]

The Binding Database is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules - [e]

BMRB's mission is to collect, archive, and disseminate (worldwide in the public domain) the important quantitative data derived from NMR spectroscopic investigations of biological macromolecules - [e]

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 - [e]

Biological Macromolecule Crystallization Database and the NASA Archive for Protein Crystal Growth Data - [e]

BioMagResBank. A Repository for Date from NMR Spectroscopy on Proteins, Peptides and Nucleic Acids - [e]

The Comprehensive Enzyme Information System - [e]

Cambridge Crystallographic Data Centre
CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high-quality information services and software - [e]

A hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H) - [e]

A Conserved Domain Database and Search Service - [e]

... is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms - [e]

Dali server
... is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is emailed back to you - [e]

DExH/D protein database
... is an attempt to gather information about the DExH/D protein family with particular emphasis on the biochemical and functional characteristics of these proteins - [e]

The DIP (TM) database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions - [e]

DSSP database
... is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries - [e]

EMBL Nucleotide Sequence Database
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications - [e]

EMBL-Align Multiple Sequence Alignment Database
Sequence alignment data - [e]

... is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided - [e]

ExPASy Molecular Biology Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE - [e]

... a database for proteins with an experimentally verified function - [e]

Provides sequence similarity searching against nucleotide and protein databases using the FASTA programs. FASTA can be very specific when identifying long regions of low similarity especially for highly diverged sequences. You can also conduct sequence similarity searching against complete proteome or genome databases using the FASTA programs - [e]

Molecular Class-Specific Information System (MCSIS) project - [e]

The Human Myocardial Two-Dimensional Electrophoresis Protein Database is the two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database for human heart proteins. It contains data on proteins identified on the 2-D PAGE maps of ventricle and atrium of human heart - [e]

... is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them - [e]

The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on - [e]

... is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species - [e]

IMGT/HLA Sequence Database
... provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT) - [e]

The Intein Database and Registry - [e]

... is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences - [e]

... stores knowledge about intermolecular interactions in the form of scatterplots - [e]

Kyoto Encyclopedia of Genes and Genomes - [e]

KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database currently consisting of COMPOUND, DRUG, GLYCAN, REACTION, RPAIR, and ENZYME databases - [e]

Ligand Gated Ion Channel Database
Ligand-Gated Ion Channels are transmembrane proteins that can exist under different conformations, at least one forming a pore through the membrane connecting the two neighbour compartments - [e]

... contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics - [e]

MEROPS database
... is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them - [e]

... is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases - [e]

Metalloprotein Site Database & Browser
MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics - [e]

... focuses on experimentally verified protein interactions mined from the scientific literature by expert curators - [e]

Molecular Informatics Resource for the Analysis of Gene Expression) is a web site dedicated to methodologies, tools, and technologies relating to gene expression information - [e]

A database of three-dimensional protein models calculated by comparative modeling - [e]

... is a biological sequence sequence comparison tool that implements the true Smith and Waterman algorithm. It runs a search on a HP/COMPAQ cluster, using single and parallelised versions of the software - [e]

Multiple sequence alignment - [e]

Comparison of PDB files which differ by point mutations - [e]

A repository of three-dimensional structural information about nucleic acids - [e]

The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease - [e]

… provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them - [e]

Peptaibol Database
A Bioinformatics resource - [e]

... is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) - [e]

... is a database of experimentally verified phosphorylation sites in eukaryotic proteins - [e]

Protein Information Resource - [e]

The Protein Kinase Resource has been redesigned and expanded with new content and cross-links with other online resources. In addition, we have introduced several new technologies to integrate information search, retrieval and visualization - [e]

Functional Genomics of Plant Phosphorylation - [e]

Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. EBI - [e]

... is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function - [e]

... is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite - [e]

... is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases - [e]

The Prosthetic groups and Metal Ions in Protein Active Sites Database - [e]

... consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them - [e]

Protein Data Bank
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease - [e]

Protein Explorer
Explore any 3D macromolecular structure model (PDB file) - [e]

Protein Kinase Resource
PKR explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior - [e]

Protein Mutant Database
PMD covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families - [e]

RCSB Protein Data Bank
A Resource for Studying Biological Macromolecules - [e]

RNase P Database
A compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information - [e]

... collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human - [e]

Protein domain library - [e]

Structural Classification of Proteins - [e]

A Database of Sensory Signal Transduction Proteins - [e]

... is a bibliographic reference data bank relative to papers dealing with sequence analysis. This data bank stores the references of articles from the expanding field of mathematical and computer analysis of biomolecular sequences - [e]

Structure Finder
... is comprised of the search interfaces and the databases developed by the NDB Project - [e]

Two-dimensional polyacrylamide gel electrophoresis database - [e]

SWISS-MODEL Repository
... is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL - [e]

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 - [e]

Protein Family Database, Release 4: Large-scale Protein Clustering based on Sequence Similarity - [e]

Telomerase Database
... is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein - [e]

The Transcription Factor Database is a database containing mouse transcription factor genes and their related genes. It is intended to select transcription factor genes nonredundantly from entire Mouse genome - [e]

... contains a complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures - [e]

On-line tool for restriction mapping nucleotide sequences - [e]

The Protein Data Bank Through Microsoft Windows. Software zur PDB-Datenbank (USA) [e] - [e]

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Software and Programs

... refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos - [e]

CLC Combined Workbench
... creates a software environment enabling users to make a large number of advanced protein, DNA, and RNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options - [e]

... is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages - [e]

... is an interface grouping eight types of programs: BLAST; MULTALIN/ CLUSTALW; DSSP; CNS; ESPript; BOBSCRIPT/ MOLSCRIPT; DINO; PHYLODENDRON; PROFIT. It aims to produce from a single PDB file four PostScript figures containing most required sequence and structure information on a protein of known structure - [e]

ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences - [e]

ExPASy Proteomics Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE - [e]

ExPASy Tools
ExPASy Proteomics tools - [e]

The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy - [e]

The Integrated Protein Literature Information and Knowledge has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development - [e]

… is a program that predicts the conformation of protein side chains. It does so either using only backbone information or using additional template information about the side-chain conformations - [e]

... is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations - [e]

Open Source versions of RasMol - [e]

The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains - [e]

Protein Family Databases
Link collection - [e]

Protein Software
Download-Seite, ZDNET - [e]

Protein Software
Download - Seite - [e]

Proteome - Scaffold Software
Confident Protein Identification: Scaffold software works with SEQUEST® or Mascot® to identify proteins from mass spectrometry data. Scaffold lets you validate the mass spec results both statistically and visually - [e]

... provides links to the PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction - [e]

... is a program for molecular graphics visualisation - [e]

Software List
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease - [e]

DeepView - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface - [e]

Universal Protein Resource is the world's most comprehensive catalog of information on proteins - [e]

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Current Protein and Peptide Science
The purpose of Current Protein & Peptide Science is to present summaries of specific aspects of research involving proteins, peptides, and interactions between the enzymes, especially proteases; the binding interactions of hormones and their receptors; the properties of transcription factors and other molecules that regulate gene expression; the reactions leading to the immune response; the process of signal transduction; the structure and function of proteins involved in the cytoskeleton and molecular motors; the properties of membrane channels and transporters; and the generation and storage of metabolic energy. Bentham - [e]

Current Proteomics
... publishes review articles in all aspects of the fast-expanding field of proteomics. All areas of proteomics are covered together with the methodology, softwares, databases, technological advances and applications of proteomics, including functional proteomics. Bentham - [e]

EMBO Journal
... provides for rapid publication of full-length papers describing original research of general rather than specialist interest in molecular biology and related areas - [e]

... is an international journal presenting original contributions on the chemistry, biochemistry, neurochemistry, endocrinology, gastroenterology, physiology, and pharmacology of peptides, as well as their neurological, psychological and behavioral effects. Elsevier - [e]

Protein and Peptide Letters
... publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Bentham - [e]

Protein Engineering Design and Selection
PEDS publishes research papers and review articles relevant to the engineering, design and selection of proteins for use in biotechnology and therapy, and for understanding fundamental properties of activity, stability, folding, misfolding and disease. Oxford University Press - [e]

Protein Expression and Purification
... is dedicated to providing a forum for information about protein isolation based on conventional fractionation as well as techniques employing various molecular biological procedures to increase protein expression. Elsevier - [e]

Protein Science
... serves as an international forum for publishing original reports on proteins in the broadest sense. The Journal aims to unify this field by cutting across established disciplinary lines and focusing on “protein-centered” science. The Protein Society - [e]

Proteins: Structure, Function, and Bioinformatics
... publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. Wiley-Interscience - [e]

... is the premier international source for information on all aspects of applications and technologies in proteomics. Wiley-Interscience - [e]

Regulatory Peptides
... provides a medium for the rapid publication of interdisciplinary studies on the physiology and pathology of peptides of the gut, endocrine and nervous systems which regulate cell or tissue function. Elsevier - [e]

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News Archive

Hemoglobin uncovered
Researchers at the BSC and the IRB Barcelona unveil crucial information about the protein transporter of oxygen, which opens up the possibility to optimize its function by introducing modifications. The study is published in the scientific journal Proceedings of the National Academy of Sciences. - [e]

Scientists get first look at how water 'lubricates' proteins
Scientists are one step closer to understanding how proteins move when they perform functions essential for supporting life. For the first time, scientists have directly observed how water lubricates the movements of protein molecules to enable different functions to happen. - [e]

The terahertz dance of water with proteins
It is in particular the type of fold that determines the function of proteins - this is a dynamic process that takes place very quickly. Up to now, the investigation of this protein 'dance' has ignored its dancing partner: Water. This interplay between water and proteins has now been observed using terahertz spectroscopy. This has enabled them to demonstrate for the first time that proteins influence the movements of the surrounding water network over a broad area. Some 1000 water molecules are "brought into line" by one protein: If their movement without protein more closely resembles a bunch of unchoreographed disco dancers, then in the vicinity of a protein it looks more like they are dancing a minuet. - [d, e]

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Research facilities and departments

Max Planck Research Unit for Enzymology of Protein Folding
Research focuses on the principles of conformational changes controlling the biological activity of peptides and proteins - [e]

Protein Structure Factory
PSF is established to characterize proteins encoded by the genes or cDNAs available at the Berlin Resource Center of DHGP - [d, e]

Other notes:

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Related Books and Scientific Literature: Proteins:


Roger L. Lundblad

The Evolution from Protein Chemistry to Proteomics: Basic Science to Clinical Application

Largely driven by major improvements in the analytical capability of mass spectrometry, proteomics is being applied to broader areas of experimental biology, ranging from oncology research to plant biology to environmental health. However, while it has already eclipsed solution protein chemistry as a discipline, it is still essentially an extension of classical protein chemistry, owing much of its maturation to prior contributions. Unfortunately, this debt is not always evident in current literature. The Evolution from Protein Chemistry to Proteomics: Basic Science to Clinical Application, in providing a different perspective than other reviews, strengthens the connection between solution protein chemistry and proteomic technology. Towards this end, Roger Lundblad, a long-time leader in protein chemistry and a scientist who has worked in both academics and industry, brings together some seemingly disparate areas into a single volume. Discussing analytical proteomics, expression proteomics, and clinical proteomics (biomarker identification), he provides coverage that is uniquely rich in detail. Lundblad applies this detail to sample preparation for proteomic analysis, including preparation from blood and tissues. He also presents specifics on the prefractionation of samples used to identify specific subproteomes such as phosphoproteomes and glycoproteomes. Comprehensive reviews are provided covering the chemical modification of proteins, including its use for chemical proteomics. Special attention is given to challenges that impede the identification, validation, and development of biomarkers into clinically useful diagnostic analytes. A bestselling author, Lundblad utilizes classical protein chemistry literature in providing an intellectual basis for proteomics that merges current concepts with the existing literature, while providing the technical detail necessary for the effective commercialization of proteomics.

CRC; 2005


Jack Kyte

Structure in Protein Chemistry

The second edition of Structure in Protein Chemistry showcases the latest developments and innovations in the field of protein structure analysis and prediction. The book begins by explaining how proteins are purified and describes methods for elucidating their sequences of amino acids and defining their posttranslational modifications. Comprehensive explanations of crystallography and of noncovalent forcesDLionic interactions, hydrogen bonding, and the hydrophobic effectDLact as a prelude to an exhaustive description of the atomic details of the structures of proteins. The resulting understanding of protein molecular structure forms the basis for discussions of the evolution of proteins, the symmetry of the oligomeric associations that produce them, and the chemical, mathematical, and physical basis of the techniques used to study their structures. The latter include image reconstruction, nuclear magnetic resonance spectroscopy, proton exchange, optical spectroscopy, electrophoresis, covalent cross-linking, chemical modification, immunochemistry, hydrodynamics, and the scattering of light, X-radiation, and neutrons. These procedures are applied to study the folding of polypeptides and the assembly of oligomers. Biological membranes and their proteins are also discussed. Structure in Protein Chemistry serves as a comprehensive textbook for advanced undergraduates and graduate students, as well as a useful reference for professionals.

Garland Science; 2006

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