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Breakdown of Page Contents
  • Journals
  • Granting Agencies
  • Supplies
  • Crystallography
  • DNA and Protein Sequences and Tools
  • Miscellaneous
Journals (in alphabetical order)
Acta Crystallographica Section D- Biological Crystallography
Applied and Environmental Microbiology
Analytical Biochemistry
Biochemical and Biophysical Research Communications (BBRC)
Biochemistry
Biophysical Journal
Biotechnology and Applied Biochemistry
Cell
Cell Host and Microbe
Critical Reviews in Microbiology
Current Opinion in Structural Biology
EMBO Journal
EMBO Reports
FEBS Journal
FEBS Letters
FEMS Microbiology Ecology
Journal of Bacteriology
Journal of Biological Chemistry (JBC)
Journal of Biochemistry
Journal of Cell Biology (JCB)
Journal of Computer-Aided Molecular Design
Journal of Molecular Biology (JMB)
Journal of Structural Biology
Journal of the American Chemical Society (JACS)
Microbiology
Molecular and Cellular Biology (MCB)
Molecular and Cellular Proteomics (MCP)
Molecular Biology of the Cell (MBoC)
Molecular Microbiology
Nature
Nature Cell Biology
Nature Reviews Molecular Cell Biology
Nature Structural and Molecular Biology
Proceedings of the National Academy of Sciences USA (PNAS)
Protein Engineering Design and Selection (PEDS)
Protein Science
Proteins
Research in Microbiology
Science
Traffic
Trends in Biochemical Sciences
Trends in Cell Biology
Granting Agencies
Grants.gov: public service to find and apply for federal grants
HHMI:
Howard Hughes Medical Institute
NIH: National Institutes of Health
NSF: National Science Foundation
Supplies

General Lab Supplies

Fisher
MidSci
P212121
Research Products International
Sigma-Aldrich
VWR

Molecular Biology Supplies

Bio-Rad
EMD4 Biosciences (combined Calbiochem, Novabiochem, Novagen)
Eppendorf
GE Healthcare
Invitrogen
IDT (Integrated DNA Technologies)
Millipore
MP Biomedicals
NEB (New England Biolabs)
Qiagen
Roche

Crystallization Supplies

Hampton Research
Jena Bioscience
Douglas Instruments

X-ray Equipment

Rigaku
Oxford Cryosystems

Meetings

Gordon Research Conference

Crystallography

Crystallography Organizations

ACA: American Crystallographic Association
IUCr: International Union of Crystallography

Protein Crystallography Basics

Introduction to Protein Structure
Amino Acid Information: Structures, chemical properties, post-translational modifications, etc.
Crystallography 101
: An introduction to the basic principles of macromolecular crystallography
Teaching and Education: Many sources for the learning of X-ray crystallography
Crystallography Made Crystal Clear: Textbook of crystallography (available on web)

Data Collection

Lawrence Berkley National Laboratory's Center for X-Ray Optics

Technical Knowledge Resources

Protein Data Bank (PDB): Structures of all proteins, nucleic acids, and complexes published to date
X-Ray Absorption Edges

X-Ray Anomalous Scattering: For MAD data

Software and Online Services

Apropos Atlas of Protein Side Chain Interactions Autodock: Predicts how small molecules bind to a 3D macromolecular structure
Cambridge Structural Database: Small molecule structures
Catalytic Site Atlas: Information on catalytic residues of crystallized proteins
CATH: Database and classification of protein domain structures
CORINA: Generates 3D models of small drug-like molecules
Crystallography and NMR System
(CNS): Crystallography and NMR structure solving
DockVision: Combines several algorithims for molecular docking
Enzyme Structures Database
ExPaSy: Contains many helpful tools and calculators for proteins
GRASP: Program for displaying and manipulating surfaces and electrostatic properties
HIC-UP: Heterocompound Information Center for small molecules
JenaLib: Database of hetero compounds
JenaLib Periodic Table: Lists all hetero compounds containing each element
Ligand Database: Ligand chemical database
LIGPLOT: Automatically plots protein-ligand interactions
MolScript: Program for displaying 3D macromolecular structures
Molecular Surface Computation: Calculates solvent-excluded surfaces
Molecular Surface Package: Calculates surface areas, volumes, curvatures
molmovdb: Database of macromolecular movements and flexibility
O
: Software to model, build, and display macromolecules
O manual
Occluded Surface (OS): Calculates spaces of atoms close together and atomic packing
Patrick Flemming home page: Links to different software, good lecture on surface analysis
PRINTS: Database of conserved motifs in protein families
Procheck: Check the stereochemistry of protein models
Procheck manual
PyMol: Displays macromolecules and creates 3D animations
Rasmol: Molecular graphics visualization program
Raster3D: Tools for generating high-quality images of proteins and other macromolecules
SOLVE/RESOLVE
: Automated structure solutions, density modification and model building
SURFNET: Calculates surfaces and void regions etc. from PDB files
TNT: Software package to refine macromolecular models
Uppsala Software
: Software and resources for crystallography and structural biology
Vega: Several molecular modeling and dynamics software programs
Visual Molecular Dynamics (VMD): Displays, analyzes, and animates macromolecules
What If: LINUX software for macromolecular modeling
Xray View
: Several programs developed by the Phillips lab at University of Wisconsin-Madison


DNA and Protein Sequences and Tools

Biocomputing: Several protein sequence analysis tools from UCL in London
CINEMA: Color INteractive Editor for Multiple Alignments, aligns multiple protein sequences
HMMTOP: Software that predicts topology of proteins and possible transmembrane helices
Homology modeling: complete notes for course
Membrane proteins: a great deal of general information from Dr. White at UC Irvine
NCBI: National Center for Biotechnology Information, contains sequences, publications, and tools
NICKPRED: Program to precict the limited proteolysis of proteins
OWL: Composite of four protein sequence data banks

Miscellaneous

Ph.D. Comics


Copyright � Chen Research Group, Department of Molecular and Cellular Biochemistry, Indiana University
Maintained by Adhitya Balaji (last updated May 23, 2020) Back to previous page