BATEMAN'S BIOCHEMISTRY HOTLIST
Analysis tools I frequently use. It's not pretty, but it originated before most college students were born.
Feel free to link to this page and email me (betabarrel@gmail.com) with your favorites.
Personal Homepage
Department
Homepage CoST
Homepage
Sequence Tools
- PUBMED - Search
tool for the National Library of Medicine
EXPASY TOOLS - Swiss site with
many protein tools- BLAST - The sequence homology
search tool
- ENTREZ - another multipurpose
search tool for NCBI
- Highwire press - another portal
into many scientific journals
- Two other web tools for searching the scientific world are Scirus
and Google Scholar
Structure Tools
- Kinemage-Related Links
- Official Kinemage Homepage-
molecular visualization software
- Download Mage,
Prekin,
KiNG (KInemage
Next Generation) - a zipped file with Prekin for windows is HERE
- Kinemage authorship ricin tutorial using KiNG
- Download demo5_4a.kin
- Kinemage Authorship Homepage
- Description
of Mage in the NCBI Molecular Modeling Database
Publications related to Kinemage Authorship and Assessment
Richardson, D. C.; Richardson, J. S. Teaching Molecular
3-D Literacy. Biochem. Mol. Biol. Educ. 2002, 30 (1), 21–26.
Bateman, Jr., R.C., Booth, D., Sirochman, R., Richardson, J., Richardson, D. (2002) Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry. J. Chem. Ed. 79, 551-552.
Booth, D., Sirochman, R., Richardson, J., Richardson, D. and Bateman, Jr., R.C. (2005) Assessment of Molecular Construction in Undergraduate Biochemistry. J. Chem. Ed. 82, 1854-1858.
Stieff, M., Bateman, Jr., R.C., and Uttall, D.H. (2005) Teaching and learning with three-dimensional representations. In J. K. Gilbert (Ed.), Visualization in science education (pp. 93-120). Oxford: Oxford University Press.
Craig, P.A. and Bateman, Jr., R.C. (2010) A Proficiency Rubric for Biomacromolecular 3D Literacy. Spring 2010 PDB Newsletter.
Link for PDB Newsletter readers interested in the biomacromolecular 3D literacy rubric.
Structure Databases
- PDB Homepage - official homepage
of the Protein Data Bank at Research Collaboratory for Structural Bioinformatics
(RCSB)
-
-
- More on Teaching with Macromolecular Visualization Tools
Assessment of macromolecular 3D literacy - a set of benchmarks intended to serve as a starting point for the development of grading rubrics at levels appropriate to student. Please email me at robert.bateman@usm.edu (or my collaborator Paul Craig at paul.craig@rit.edu) if you use this with your courses or would like to make a suggstion.
FoldIt - protein folding game
Immune Attack - Ok, it is not strictly a protein game but it is really neat.
Other Structure Tools (I'm open to suggestions.)
Superimposition tool SuperPose
PDB
beta listing of structure visualization tools
MolviZ.Org
- molecular visualization resources collected by Eric Martz
Protein Explorer Homepage - frames-based
protein analysis using a Chime or Jmol base
Swiss-Model - generate
a model of your sequence based on the structure of a homologous protein. The
Swiss PDB Viewer (Deep View) can also be downloaded.
RasMol homepage - another
type of molecular visualization software. Also see www.openrasmol.com
.
RasTop is a molecular visualization software for Windows platforms
adapted from the program RasMol, initially developed by Roger Sayle. RasTop wraps a user-friendly graphical interface
around the "RasMol molecular engine".
Jmol is a free, open source molecule viewer written in Java.
PyMOL is a USER-SPONSORED molecular modeling system with an OPEN-SOURCE
foundation.
UCSF Chimera is a highly extensible, interactive molecular
graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to
maximize extensibility and leverage advances in hardware. UCSF Chimera is available free of charge for academic,
government, non-profit, and personal use.
MOLMOL is 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. The program runs on UNIX and Windows NT/95/98/2000
and is freely available.
Cn3D is a helper application for your web
browser that allows you to view 3-dimensional structures from NCBI's Entrez
retrieval service. Cn3D runs on Windows, MacOS, and Unix. Cn3D simultaneously displays structure, sequence, and
alignment.
ICM Browser has all the
standard features of a robust molecular graphics program (CPK, solid ribbon,
balls-and-sticks, wire, dot surfaces, coloring by property, etc). In addition,
ICM Browser supports many other features not offered by other programs, such
as manual docking, interactive model building, perspective, interactive zoom,
independent clipping planes, eight switchable and combinable image buffers,
flexible secondary structure assignment, chemical bonds or topological trees,
image annotation, multiple object loading and display, and selection of atom/residue/molecules
by types and patterns.
VMD is a molecular visualization program for displaying,
animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
MolScript is a program for displaying molecular 3D structures,
such as proteins, in both schematic and detailed representations.
gOpenMol can be used for
the analysis and display of molecular dynamics trajectories and the display
of molecular orbitals, electron densities and electrostatic potentials from
programs like the GaussianXX, PC GAMESS and Jaguar.
DINO is a realtime 3D visualization program for structural biology
data. It runs under X-Windows and uses OpenGL. Supported architectures are IRIX, Linux (i386 and PPC), OSF1 and
SunOS. DINO is distributed in binary form only, the current DINO version is 0.9.1.
YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X.
Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
World Index of BioMolecular Visualization Resources includes above and more.
Homepages of Biochemical Educators using Structure Tools
Jane and David Richardson
Gale Rhodes
Eric Martz
Charles Grisham
William McClure
J.
Ricky Cox
Duane
Sears
Brian White