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
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