Membrane Biophysics Resources

Molecular Dynamics Simulations of Membranes

Prepared by Peter Tieleman at the University of Calgary. The PDB coördinates of numerous molecular dynamics simultions are available, including micelles, bilayers, and membrane proteins.

Molecular Dynamics Simulations of Lipid Bilayers

Simulations from the Scott Feller Laboratory at Wabash College. This site provides, among other things, PDB coördinates of lipid bilayers produced by molecular dynamics simulations.

Molecular Dynamics Simulations of POPC

Helmut Heller, of the Leibniz-Rechenzentrum in Munich, provides molecular dynamics simulations of POPC in various phases.

Lipid Bilayer Membranes for RasMol

This page at the University of Massachusetts PDB files are available for 1-palmitoyl 2-oleoyl phosphatidyl choline bilayers (200 molecules total), hydrated with about 15 layers of water on each side, for various configurations.

Transport Protein Database

The Saier Laboratory Bioinformatics Group at UCSD provides the TC-DB website, which details a comprehensive classification system for membrane transport proteins known as the Transport Commission (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 300 families of transport proteins are provided.

Protein Sequence Analysis And Modeling (PSAAM) Software

This package, from the University of Illinois, contains a main program (PSAAM), and several ancillary programs (INFORMAT, calculates mean sequence profiles and mutability moment (conservation moment) from aligned sequences; FINDSEQ, will find sequence strings (structural motifs, binding domains, etc.) in a sequence file, or a directory of sequence files; GENBANK, will extract sequence data from a file saved from Entrez).

Membrane Protein Secondary Structure Prediction

The purpose of this server at the University of Split, Croatia, is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions.

DMPC (Database of Membrane Protein Contacts)

DMPC, the Database of Membrane Protein Contacts, is a regularly updated database that provides visualization, derivation of structure based amino acid propensity scales from the entries, and analysis of amino acid composition, hydrogen bonds, packing densities and packing defects to assess structure function relationships of helical membrane proteins.

 

Proteins WWW Resources

Protein Data Bank

The Protein Data Bank from the Research Collaboratory for Structural Bioinformatics (RCSB)

Protherm: Thermodynamic Database for Proteins and Mutants

ProTherm contains numerical data of several thermodynamic parameters, namely, Gibbs free energy, enthalpy, heat capacity, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins upon mutations. It also contains information about secondary structure, accessibility of wild type residues, experimental conditions (pH, temperature etc.), measurements and methods used for each data, and activity information (Km and kcat etc.).

PDB Reports at EMBL

Comprehensive report of errors in PDB files from the Sander group at Heidelberg.

Molecules To Go Protein Data Bank via the NIH

An especially convenient interface for accessing PDB data.

San Diego Supercomputer Center Biology Workbench

A point and click web interface located at NCSA that provides access to databases and analysis tools for biological investigations of proteins and nucleic acids.

Molecular Biology Protocols and Bioinformatics

A portal for molecular biology which contains methods and protocols, bioinformatics, and news categorized by DNA, RNA, protein, and proteomics. Also discuss and ask questions about molecular research techniques in the forum.

PIR the Protein Information Resource

An integrated protein information resource for genomic and proteomic research. Provides access to UniProt (Universal Protein Resource).

Swiss-Prot: an Annotated Protein Sequence Database from ExPASy

Swiss-Prot provides a high level of annotations such as: the description of the function of a protein, its domains structure, and post-translational modifications, variants, etc. There is a minimal level of redundancy and a high level of integration with other databases.

Center for Molecular Modeling at the NIH

A centralized source of information about molecular modeling methods and biological applications. Includes access to Molecules To Go, an especially convenient interface for accessing PDB data, and PDB at a Glance, which organizes the Brookhaven PDB according to Functional Classes.

NCBI Structure Group at the NIH

Included are links to NCBI's MMDB - Molecular Modeling DataBase, PubVast, PubChem, and conserved domain database (CDD).

RasMol Molecular Visualization at the University of Massachusetts

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK.

DeepView - Swiss-PDBViewer for Visualization of Protein Structures at ExPASy

DeepView - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse 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.

GenBank at the National Center for Biotechnology Information

Search MEDLINE, protein databases, and nucleotide databases using Entrez Browser with forms-based or non-forms based clients.

HIV Sequence Database at the Los Alamos National Laboratory

The Human Retroviruses and Aids Database collects, curates, analyzes, and publishes genetic sequences of the human immunodeficiency virus (HIV) and related species. All HIV and related viral sequences and alignments are available via anonymous ftp at ftp-t10.lanl.gov in directory /pub/aids-db.

National Center for Genome Resources

NCGR offers an integrated biological knowledge system facilitating organized accessibility, integration, and analysis of different biological data types. This system provides the research community with a framework for determining the function of gene sequences.

Center for Biological Sequence Analysis

A research site with a goal to obtain knowledge of the complex relations between sequence composition and macromolecular structure and function. The research is aimed at creating entirely new possibilities in the study of evolutionary processes by comparison of sequence patterns across species. The work of the center focuses in particular on a number of novel data driven and adaptive computational methods, which are not created on the basis of assumptions and known facts, but for example by training of artificial neural network algorithms.

SCOP from MRC

SCOP organizes the Brookhaven PDB according to secondary, tertiary, and other structural features. It is produced at MRC Laboratory of Molecular Biology and the Cambridge Center for Protein Engineering.

Atlas of Side-chain and Main-chain hydrogen bonding

A graphical summary of hydrogen bonding in a dataset of high-resolution protein structures. Distributions of the frequencies and geometries of hydrogen bonds formed by main-chain and side-chain donors and acceptors are available.

Oxford Laboratory of Molecular Biophysics

Access to Crystallographic Web Server and much more!

Principles of Protein Structure from Birkbeck College

This is a course available on the Internet which is sponsored by Birkbeck College. The course uses a wide range of interactive and multimedia techniques to bring high-quality, low-cost learning to students throughout the world. The course is intended for scientists who need to know more about how and why protein structure is central to modern biology. The Protein Structure Course Announcement provides a course outline for committed scientists in disciplines such as chemistry, molecular biology, pharmacology, and immunology who wish to understand how the three-dimensional structures of proteins are critical to their functions.

Protein Motions a Protein Data Bank Listing

This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.

European Bioinformatics Institute (EBI)

EBI is an Outstation of the European Molecular Biology Laboratory. Links to the Human Genome Mapping Project and Nucleotide Sequence and several Protein Sequence Databases as well as Sequence Similarity Searches and Database query and retrieval are available.

 

Other Useful WWW Resources

The Library of Congress

Access to the Library of Congress WWW server

World Factbook

World atlas and almanac information from the CIA

PubMed Medline Database

Search the National Library of Medicine Medline Database.

Visible Human Viewer at Northeast Parallel Architectures Center (NPAC)

Using a Java applet, select and view high-resolution images of 2-dimensional slices of a human body, using image data taken from the National Library of Medicine's Visible Human Project. See also Visible Human Server.

 

Californiana

Californiana - For Surfers:

Live camera feed from Newport Beach pier, with current conditions and forecast.

Menus of pages like the above, for all of Southern California.

Forecast information, with extensive maps of buoy-type swell data for Southern California and the Eastern Pacific.

For Movie Fans:

Movie Trailers and access to all sorts of other movie information.

All Media Guide: Search a database for details of modern and classic films.

Fandango Movie and Entertainment Site

For Art Lovers:

J. Paul Getty Museum "The J. Paul Getty Museum's collection was begun by businessman, collector, and philanthropist J. Paul Getty (1892-1976) who viewed art as an enlightening influence."..."The Museum's holdings include Greek, Roman, and Etruscan antiquities; European drawings, paintings, illuminated manuscripts, sculpture, and decorative arts dating to 1900; and American and European Photographs, from the 19th century to the present."

Louvre Museum, Paris It's not Californiana, but who can resist the Louvre?!

For Commuters:

Real-time freeway traffic conditions from CalTrans