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learning
crystallography
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Introduction of protein crystallography
Multiple wavelength Anomalous Diffraction(MAD)
Theory and methods of data analysis
Space groups
Anomalous dispersion
Reciprocal cell calculation
Protein crystallography on the web |
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crystallization
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Pictorial library
Hampton research
Emerald biostructure
Crystallization database
Guide to crystallization
Practical guide of crystallization |
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data
processing & scaling
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d*TREK
HKL Package
MOSFILM in CCP4
Strategy of processing
Example of Mosflm and SCALA
Autoindexing with DENZO
HKL manual |
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heavy
atom search
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Heavy atom databank
Heavy atom library
About Xenon
Procedure of derivative |
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phasing
& refinement
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ARP/wARP A system for the refinement of
protein structures via automatic updating and re-building of the model
and solvent structure
CCP4 A suite of programs covering all aspects of crystallographic
structure determination, refinement and analysis
CHART Automatic Structure Solution
CNS A system for structure determination from crystallographic or
NMR data
PHASES Compute phase angles for diffraction data from macromolecular
crystals
SAPI heavy atom search program using direct methods
SHELX A set of programs for direct structure solution and refinement
with high resolution diffraction data
SHARP
SNB dual-space direct-methods procedure for determining crystal structures
from X-ray diffraction data
SOLVE An automated system for phase determination from MIR and MAD
data
TNT
XtalView An interactive system for building and manipulating models
in electron density map and for phase determination from MIR or MAD
data.
USF software O related softwares in Uppsala Software Factory |
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modeling
& graphics
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ARP/wARP An automatic model building program
MAIN
An interactively driven suite of programs for molecular modeling,
density modification, model refinement and structure analysis
O
An interactive system for building and manipulating models in electron
density maps
XtalView An interactive system for building and manipulating models.
HiCUP
Ligand database
prodrg
.pro .top file generation
corina
Ligand drawing
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molecular
replacement
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MR tutorial from data to density
Amore in CCP4
BEAST in CCP4
EPMR
MOLREP in CCP4
Queen of Spade
GLRF
MRX |
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picture
drawing
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Alscript sequence alignment and drawing
BioEditor A tool for creating and viewing dynamic, formatted structure
annotations; for Windows
Bobscript
DINO 3D visualization program for structural biology data
GRASP
ProteinScope Free viewer to display and manipulate PDB files and create
animations and slides of proteins
Pymol
Rasmol
Molmol
Molray
Molscript
Raster 3D
Ribbons A program for molecular illustration and error analysis
SPOCK
VMD Visual Molecular Dynamics
Chimera
MSMS a molecular surface computation
MEAD Macroscopic Electrostatics with Atomic Detail
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structure
evaluation
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Biotech Validation Suite
ERRAT Structure Submission Page
PROCHECK
Verify3D Structure Evaluation Server
WHAT_CHECK |
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structure
analyses
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ASC The Analytic Surface Calculation Package
The ASTRAL compendium Databases and tools useful for analyzing protein
structures and their sequences
CAST A Server for Identification of Protein Pockets & Cavities
CastP Server that calculates measurements of structural pockets and
cavities of proteins and nucleic acids
CATH Class, architecture, topology and homologous superfamily
CE/CL Alignment server and databases for structure comparison by Combinatorial
Extension (CE) and Compound Likeness (CL)
CAMPASS CAMbridge database of Protein Alignments organized as Structural
Superfamilies
ConSurf Server for the Identification of Functional Regions in Proteins
by Surface-Mapping of Phylogenetic Information
Culled PDBM Representative PDB structures
DALI Comparison of protein structures in 3D
DSMP Database of Structural Motifs in Proteins
eF-site Electrostatic-surface of Functional site
Grass Graphical Representation and Analysis of Structure Server
HIC-Up Hetero-compound Information
HOMSTRAD Homologous Structure Alignment Database
IMB Jena Image Library of Biological Macromolecules Provides information
on sites included in three-dimensional biopolymer structures
IMB Jena Image Library Site Database Provides information on sites
included in three-dimensional biopolymer structures
Library of Protein Family Cores
Ligand-Protein Contacts and Contacts of Structural Units A resource
which provides an analysis of interatomic contacts in ligand-protein
complexes (LPC) or an analysis of interatomic contacts in protein
entries (CSU)
Macromolecular Structures Database
Morphology of Protein-Protein Interfaces A visual survey of protein-protein
interfaces in homodimeric proteins from the PDB
NRL 3D Sequence-Structure Database produced by PIR
OLDERADO On Line Database of Ensemble Representative And DOmains
PALI Phylogeny and ALIgnment of homologous protein structures
PartsList Dynamic protein fold ranking by disparate attributes, including
whole-genome expression and interaction information
PDB select Representative PDB structures
PDBSum Summaries and structural analyses of PDB data files
PQS EBI MSD Protein Quaternary Structure database
SCOP Structural Classification of Proteins (UK), mirrored around the
world
SCOR Structural Classification Of RNA
Protein Sidechain Webpage Information on sidechain conformational
analysis, sidechain rotamer libraries, and sidechain conformation
prediction
STING Sequence To and withIN Graphics (USA), mirrored in Israel
SPIN-PP Surface Properties of Interfaces - Protein Protein interfaces
TOPS-Protein Topology |
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synchrotron
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Structural biology synchrotron users organization
biosync
ALS - Advanced Light Source
CAMD/LSU Synchrotron
DESY, EMBL- Hamburg
ESRF, EMBL- Grenoble
Gulf Coast Protein Crystallography Consortium
NSLS X-8C
NSLS X-12C
Photon Factory (Protein Crystallography)
Pohang accelerator laboratory
Beamline 6B of pohang accelerator laboratory
Spring-8 |
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others
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