Structure Analysis

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Biology and Databases

StructuralBiologyKnowledgebase
RCSB PDB
GenomeNet WWW server
ExPASy Molecular Biology Server
- ExPASy - Tools
- ExPASy - ProtParam tool
- BoxShade Server · prety printing of aligned sequences
NIG Homepage [ Research Tools ]
ENDscript 2 · graphical representation of the primary to quaternary structure
ESPript 3 · graphical representation of aligned sequences
BMCD Release 7 · Biological Macromolecule Crystallization Database
Amino Acid Information
Protein Model Portal (PMP) · models computed by comparative modeling methods
ライフサイエンス辞書プロジェクト
Glycoforum

Crystallization

CCP4 Wiki -- Crystals
MPCD Marseille Protein Crystallization Database, compilation of CYCLOP and BMCD (v2.0)
BMCD Release 7 · Biological Macromolecule Crystallization Database
Hampton Research
- Solutions for Crystal Growth
- RAMC -- Recent Advances in Macromolecular Crystallization. 2007, 2005, 1999, 1997.
XtalPred - Crystallization Predictor
Crystool by Brent Segelke
SAmBA･for making a matrix
Heavy atom derivatives and MAD
- Heavy atom derivatives･ a tutorial. DEAD
- Heavy Atom Databank
- HATODAS · Heavy-atom Database System
- X-ray Absorption Edges

Crystallography

General
- CCP4 [Main Page][ Program Documentation][ CCP4 online talks][ CCP4 Newsletters ]
- CCP4 Wiki
- Crystallography & NMR System
- XPLOR Interface Manual · 本を見るより見やすいかも．
- Computational Crystallography Initiative @LBL
- Phenix · Python-based Hierarchical ENvironment for Integrated Xtallography.
- The Clipper Project by Kevin Cowtan. a set of object-oriented libraries for crystallographers.
- Uppsala Software Factory
  - Archive · RAVE, X-UTIL(MOLEMAN2, SEAMAN), VOIDOO, DEJAVU, SPASM, SBIN. OS-Xではfinkでインストールできる．
  - HIC-Up: Hetero-compound Information Centre - Uppsala - Release 12.1 [2008-03-01]
  - Gerard "CD" Kleywegt
- Crystallography and Biocomputing @Univ Cambridge, Biochemistry, Structural Biology
  - RAPPER･an ab initio conformational search for Restraint-based protein modelling
  - RAMPAGE･Structural validation by assessment of the Ramachandran plot
  - Fugue･ for recognizing distant homologues by sequence-structure comparison.
  - Evolutionary Trace Server (TraceSuite II)･A fully automated evolutionary trace server
  - JOY･ Protein structure and alignment analysis
- CCP14 Homepage
Basics
- Bilbao Crystallographic Server
- Basic Maths Definitions for Protein Crystallographers by Eleanor Dodson.
- Les 230 groupes d'espace · [ @CCP14]･by Jean-Jacques Rousseau. (applet does not work)
- A Hypertext Book of Crystallographic Space Group Diagrams and Tables
- Crystallographic Space Group Symmetry Tables by Nikos Pinotsis.
- Direct and Reciprocal Lattice Visualizer
How-to and Courses
- Google - Crystallography > Software
- Crystallography on OS X
- BioKids Wiki
- おうちでできる構造解析 -- iMosflm
- 千田氏のIndex MIR Manual ver. 2.0
- 伏信氏のリンク集
- 伏信氏の結晶構造解析関係マニュアル
- 渡邉氏氏のマニュアル集
  - ccp4i 使用メモ - MAD data を処理する - @hokudai
  - MAD (SAD) data による位相決定からモデル構築まで Solve, Resolve, XtalView (おまけ ARP/wARP)
- CCP4 Talks ? Scala Scaling masterclass | one-day workshop at the ACA 2002 | Study Weekend 2002
- CCP4 Tutorial | CCP4 Interface Tutorial
- Local Density Correlation · how to use the local density correlation method of Randy Read to investigate structural differences between molecules. @USF
Data Collection and Reduction
- BioSync · A Structural Biologist's Guide to High Energy Data Collection Facilities
- 放射光研究施設 Photon Factory, KEK, Japan. [ Beamline Page of SBG]
- ADSC Quantum 4R, 210, and 315 Technical Comparison
- Brucker SMART, SAINT
  - SMART Quick Users Guide - SCSB - UTMB
  - SAINT Users Guide - SCSB - UTMB
  - SMART instructions, Instructions for using SMART, SAINT, ASTRO (PDF)
- DIALS: Diffraction Integration for Advanced Light Sources
- DPS · The Data Processing Suite.
- HKL Research, Inc.･ HKL2000. [Scalepack Keywords ]
- Denzo and Scalepack log Abstraction scripts. denzolog & scalepacklog. the link is unreachable.
- MOSFLM manual @Hoku-dai. unreachable.
- MOSFLM 6.2.2 User Guide @LMB
- XDS Program Package · X-ray Detector Software
- Interactive DPS/Mosflm/CCP4 Data Processing V1.32
- X-ray diffraction data collection･ course @ U-Alberta
- Bruker AXS user pages of former Nonius equipment
- Programmers manual for the Nonius python library @Bruker AXS Collect Package
- Normal probability analysis in the ccp4 talks
- Matthews Probablility Calulator server
Crystal Twinning
- CCP4: twinning
- Some PowerPoints on Twinning
Solution
- SnB Home Page
- SHELX Program Page
- Phaser
- SHARP/autoSHARP user documentation @Global Phasing ltd.
- Introduction to SHARP @Osaka-U. unreachable.
- Solve/Resolve
- Solve--Automated structure solution for MIR and MAD
Molecular Replacement
- Replace･ GRLF and TF. Drawing a self-rotaion function map.
Model building
- Coot Home Page · @CCP4 Wiki
- ARP/wARP Home Page
- TURBO_FRODO
- QUANTA 2000
  - Xray Structure and Analysis - Contents･ online manual @UCSF
  - Using X-AUTOFIT
- Xfit hardware stereo
- o-info: Mail Thread Index
- Bias removal server
- TLSMD: TLS Motion Determination Server

Utilities

scripts by Charlie Bond includes pdb-model.el for emacs.
The Dundee PRODRG Server･ convert coordinates for small molecules in PDB format to others
STAN - the STructure ANalysis server. (WASP, CISPEP, and MOLEMAN2)
The ConSurf Server. ConSurf Homepage
Crystallographic Web Applets by Bernhard Rupp.
The WHAT IF Web interface･ molecular modeling and design server
WHAT IF･ a versatile molecular modelling package
WHAT_CHECK · a stand-alone program. free.
Water molecules
- CONTACT in CCP4
- WATERTIDY in CCP4
- HBplus and LIGPLOT
- WAP: water analysis package · a Web-based package to calculate geometrical parameters between water oxygen and protein atoms
- SMS (Kyushu mirror)･ Protein Dossier and/or Contacts.
- WHAT IF･ includes functions to handle H-bonds and water molecules.
- MCFMAN･ manupulates PDB or MCF formatted files.
Molecular display and presentation
- PyMOL Home Page
- UCSF Chimera
- ccp4mg
- MOLMOL - MOLecule analysis and MOLecule display
- Protein Explorer･ web-based structure display system.
- Jmol Protein Explorer
Interactive motif and fold recognition in protein structures･ article by Gerard J. Kleywegt's group.
EBI SSM･ Secondary Structure Matching for protein structure comparison.
DEJAVU to find motifs and to recognise other proteins with a similar fold. Public server is not available now.
structure-based sequence alighnment
- Structural alignment software @Wikipedia
- SEQUOIA 1.0.1 User's Guide･ structure-based sequence alighnment.
- Fugue･ for recognizing distant homologues by sequence-structure comparison.
- Evolutionary Trace Server (TraceSuite II)･A fully automated evolutionary trace server
- JOY･ Protein structure and alignment analysis
- Homstrad･ homologous structure alignment database.
- STRAP･ Structural Alignment Program for Proteins. editor.
- Indonesia Manual･ structure-based sequence analysis.
2D topology diagram software
- TOPS･Topology Of Protein Structure server. on-line calculation and diagram genaration.
- Protein Topology Home Page･ obsolete.
- Edit Tops･ java. Software for generation, editing and viewing cartoons.
- TopDraw･ protein topology sketcher. needs a topology derived from other source, like PROMOTIF.
docking
Electrostatics and solvation
- APBS, PDB2PQR, and related software ·
Molecular Models - Labquip･ plastic molecular models.

Supplier

Emerald BioStructures
Cyber-Catalog
SIGMA-ALDRICH
同仁化学研究所
ナカライテスク　[online-catalogue]
Siyaku.Com
フナコシ
Amersham -- News Letter
Emerald BioStructures
BioCrystal Home Page
CYPRESS
信越シリコン
日本NAG株式会社ホームページ
HYDRA_スクラム_トップ
Wyatt Technology Corporation　- Laser Light Scattering
日本ジッパーチュービング · EMI対策部品．シールド．