7.88J | Spring 2015 | Graduate
Protein Folding and Human Disease

Related Resources

Here are some useful links for your searching pleasure:

Protein Data Bank - the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.

Protein Data Bank Mirror Site

PDB Search Tutorial - Protein Data Bank help section with resources on searching, browsing, reports, and general help topics.

Berman, H. M., D. S. Goodsell, and P. E. Bourne. “Protein Structures: From Famine to Feast.” (PDF) American Scientist 90 (2002): 350–9.
Publication on PDB Growth

Swiss PDB Viewer (Deepview) - an application that allows users to analyze several proteins at the same time.

UniProtKB / Swiss-Prot Release 50.6 statistics - the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.

Other Free Visualization Programs (free for academic use):

RasMol - a program for molecular graphics visualization used to view macromolecules and to prepare publication-quality images.

PyMol - an open-source molecular visualization system that can produce 3-D images of small molecules and biological macromolecules.

Chimera - a free, downloadable program for interactive visualization and analysis of molecular structures and related data.

Cn3D - a web browser-based application that allows users to view 3-D structures from NCBI’s Entrez Structure database.

iMol - a free molecular visualization application for Mac OS X; can handle multiple file formats for small and large molecules, load multiple molecules, and move and rotate molecules independently. 

JMV - a Java and Java3D based molecule viewer, which can be used alone or integrated into other programs; provides a variety of molecular representations, coloring styles, and stereoscopic rendering capabilities. 

MolView - an open-source web application for web-based data visualization; can be used for searching through various scientific databases such as compound databases, protein databases, and spectral databases.

VMD - using 3-D graphics and built-in scripting, this free and open-source program is used for molecular visualization and for displaying, animating, and analyzing large biomolecular systems.

MolMol - a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

Jonathan King Lab Homepage - Professor Jonathan King’s laboratory research answers questions about protein folding, protein misfolding, virus assembly, computational biology and we are investigating proteins from photosynthetic prokaryotes.

Protein Folding Groups List - A list of research groups interested in protein folding (updated frequently).

The Basics of Making Cheese - Overview of the basic components of cheese and the process of making cheese.

7.340 Nano-life: An Introduction to Virus Structure and Assembly - an undergraduate course that covers the basic principles of virus structure and symmetry, capsid assembly, strategies for enclosing nucleic acid, proteins involved in entry and exit, and the life cycles of well understood pathogens such as HIV, influenza, polio, and Herpes.

7.343 Protein Folding, Misfolding and Human Disease - an undergraduate course with a main focus on the protein folding field with several topics related to protein structure and design and protein aggregation diseases.

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Spring 2015
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group_work Projects
assignment Written Assignments