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Research Resources

  • 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.

  • 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 kca

  • PDB Reports at EMBL

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

  • 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.

  • 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.

  • 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.

  • 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 trai

  • 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.

  • 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

  • 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.

  • ExPASy : Bioformatics Resource Portal

    ExPASy is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. 

  • BioZon

    A unified biological resource on DNA sequences, proteins, complexes and cellular pathways.

  • Brenda - Comprehensive Enzyme Information System

    Contains functional information for nearly 5,000 enzymes. 

  • ChemSpider

    ChemSpider is a free chemical structure database providing fast text and structure search access to over 58 million structures from hundreds of data sources.

  • PubChem

    Find chemical structures, assay data points, and descriptive data about small molecules.

  • TOXNET

    Find information on toxicology, environmental health, hazardous chemicals, and toxic releases.

Teaching Resources

  • Resources for Teaching Biological Physics / Biophysics

    This web site gives an informal listing of articles on teaching biophysics, biophysics textbooks, and hyperlinks for biophysics courses nationwide, plus a few English-language sites in other countries.

  • The International Union for Pure and Applied Biophysics (IUPAB)

    The International Union for Pure and Applied Biophysics (IUPAB) is a member of the ICSU (International Council for Science) family. Affiliated to it are the national adhering bodies of more than 50 countries. Its function is to support research and teaching in biophysics. Its principal regular activity is the triennial International Congresses and General Assemblies.

  • Practical Uses of Math and Science (PUMAS)

    A collection of brief examples showing how math and science topics taught in K-12 classes can be used in interesting settings, including every day life. The examples are written primarily by scientists, engineers, and other content experts having practical experience with the material. They are aimed mainly at classroom teachers, and are available to all interested parties via the PUMAS web site.

  • The Engineering Place

    A collection of resources for teachers to use in their classrooms, put together by NC State University's College of Engineering.

  • Teach Engineering

    Curriculum for K-12 Educators: Standards-aligned engineering lessons and hands-on activities for use in science, engineering, and math classrooms.

  • USF STARS Fellows

    Current Modules being implemented in Schools Based on Sunshine State Standards.

  • ECOS

    The ECOS Program is a partnership between the University of Montana’s Division of Biological Sciencesand College of Forestry and Conservation and the Missoula County Schools Curriculum Consortium. ECOS is funded by the National Science Foundation's GK-12 Program. ECOS is aimed at enhancing teaching skills of graduate students in the sciences and promoting hands-on science education in K-12 schools.

  • CASES Online

    CASES Online is a collection of inquiry-based lessons to engage K-12 and undergraduate students in exploring the science behind real-world problems. 

  • Life Science Teaching Resource Community

    The Life Science Teaching Resource Community is an online community for life science educators at all levels.

  • Biophysics and Your Body

    Physics of the Human Body can be a tool for teachers to support students in meeting the Missouri Grade Level Expectations for Science. As a curriculum supplement, lessons in the module can be used to address gaps in existing curricular materials or enrich teachers’ instruction. As an interdisciplinary module, Physics of the Human Body can be used in diverse ways and with flexibility according to teachers’ and students’ needs.

  • Evolution and Biophysics of Coconuts

    In this experiment students investigating the physics of floating and falling coconuts, using the coconut kernel. This makes an excellent idea for looking at evolution and adaptation in an unusual context. 

  • Cornell Science Inquiry Partnerships

    Resources for science projects developed by graduate and undergraduate students in collaboration with middle and high school teachers.

K-12 Biophysics Outreach Programs & Resources

  • Saturday Morning Biophysics – Image life!

    Saturday Morning Biophysics: Image Life! is a program at Texas A&M Health Science Center that introduces middle school and high school girls to current research topics in the physical and life sciences. 

  • UIUC Biophysics K-12 Outreach

     Program pairs biophysics graduate students with local K-12 teachers to develop lessons which teach middle and high school students about the exciting research happening here at the University of Illinois, Urbana-Champaign.  

  • Physics Van

    The Physics Van is an outreach program of the University of Illinois Physics Department, part of the Illinois College of Engineering.

  • Caltech Precollege Science Initiative 

    The Caltech Precollege Science Initiative is such a collaborative effort, linking science and engineering professionals with educators, teachers, and school administrators.

  • NSF Graduate STEM Fellows in K-12 Education (GK-12) Program

    The NSF Graduate STEM Fellows in K-12 Education (GK-12) Program supports fellowships and training for graduate students in science, technology, engineering, and mathematics (STEM). Through interactions with teachers and students in K-12 schools, graduate fellows can improve communication and teaching skills while enriching STEM content and instruction for their K-12 partners.

  • SEPAL

    The Science Education Partnership and Assessment Laboratory (SEPAL) was founded in 2004 to integrate science education efforts into the Department of Biology and College of Science and Engineering at San Francisco State University. Since then, SEPAL has grown into a vibrant community of scientists. SEPAL has an active research laboratory investigating how science is learned, offers both undergraduate and graduate courses, and provides multiple opportunities for SFSU students and scientists to co

  • BEN (BiosciEdNet)

    Digital Library Portal for Teaching and Learning in the Biological Sciences Teaching and learning resources for undergraduate and graduate students from collaborating organizations in the biological sciences.

  • Science NetLinks

    Standards-based lesson plans for teachers that incorporate reviewed Internet resources and that are searchable by Project 2061 Benchmarks.

  • Science Update

    A daily, 60-second feature radio show covering the latest discoveries in science, technology and medicine since 1988.

  • ISU GK-12

    The Graduate Students in K-12 Education (GK-12) Program is a three-way partnership between ISU, local industry and K-12 schools in the greater Pocatello area. The goal of GK-12 is to improve science education in Southeast Idaho by involving K-12 students in locally relevant science and engineering activities.

Free Online Courses

  • MIT Open Courseware

    A variety of free online courses and materials at the undergraduate and graduate level, offered by MIT, including courses on biophysics, computational and structural biology, and more.

  • Khan Academy

    Khan Academy offers practice exercises, instructional videos, and a personalized learning dashboard that empower learners to study at their own pace in and outside of the classroom. They tackle math, science, computer programming, history, art history, economics, and more.

Other Resources

  • Resources for Minorities in Science- compiled by Oregon State University

    A list of various resources for minorities in science.

  • Minorities to Majorities

    Platform connecting under-represented ethnic minority, female, LGBTQ+ and international students with scholarships, internships, fellowships and more.

  • Científico Latino

    Científico Latino aims to improve diversity in STEM by providing resources to undergraduates and graduate students in STEM fields. The website regularly updates lists of fellowships and scholarships, sample essays for graduate school applications and fellowships, and blog posts related to being a successful professional in STEM. Científico Latino focuses on providing pertinent information for underrepresented students, but the site contains resources for everyone, underrepresented or

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