Structural Biology Group Pavia - Crystallography Links

Some Useful Links:

Tutorials about X-Ray Crystallography:

A Protein Crystallography Course

http://www-structmed.cimr.cam.ac.uk/course.html

Protein Crystallography Tutorial Site (Crystallography 101)

http://www.ruppweb.org/Xray/101index.html

Interactive Tutorial about Diffraction

http://www.mineralogie.uni-wuerzburg.de/crystal/teaching/teaching.html

Webmineral - The different crystal froms

http://webmineral.com/crystall.shtml

Crystallography Softwares:

MOSFLM

http://www.mrc-lmb.cam.ac.uk/harry/mosflm/

CCP4

http://www.ccp4.ac.uk/

Coot

http://www.ysbl.york.ac.uk/~emsley/coot/

Molscript

http://www.avatar.se/molscript/

Bobscript

http://www.strubi.ox.ac.uk/bobscript/

Raster3D

http://www.bmsc.washington.edu/raster3d/raster3d.html

Pymol

http://pymol.sourceforge.net/

Ligplot

http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

http://www.imsb.au.dk/~mok/o/

ARP/wARP

http://www.embl-hamburg.de/ARP/

SHELX

http://shelx.uni-ac.gwdg.de/SHELX/

GRASP

http://trantor.bioc.columbia.edu/grasp/

APBS

http://apbs.sourceforge.net/

JMOL

http://jmol.sourceforge.net/

BUSTER-TNT

http://www.globalphasing.com/buster/

SHARP

http://www.globalphasing.com/sharp/

Rasmol

http://www.bernstein-plus-sons.com/software/rasmol/

UCSF Chimera

http://www.cgl.ucsf.edu/chimera/

SITUS

http://situs.biomachina.org/

TLSMD

http://skuld.bmsc.washington.edu/~tlsmd/

Sequence/Structure Databases:

The Protein Data Bank

http://www.pdb.org/

Cambridge Structure Database

http://www.ccdc.cam.ac.uk/

BLAST

http://www.ncbi.nlm.nih.gov/BLAST/

ELM

http://elm.eu.org/about.html

GlycoSciences

http://www.glycosciences.de

Computational Tools for Crystallography on the Web:

High Resolution Space Group Diagrams and Tables

http://img.chem.ucl.ac.uk/sgp/large/sgp.htm

Dundee ProDRG server

http://davapc1.bioch.dundee.ac.uk/prodrg/

Energy Wavelength Frequency Converter

http://heasarc.gsfc.nasa.gov/cgi-bin/Tools/energyconv/energyConv.pl

Heavy Atoms Energies for SAD/MAD phasing

http://www.chem.gla.ac.uk/protein/mirror/stura/heavy.html

Bioinformatic Tools for Protein Biochemistry & Molecular Biology:

ExPASy (Expert Protein Analysis System) server

http://expasy.org/

An interactive Periodic Table of the Elements

http://www.webelements.com

Sequence Manipulation Suite 2

http://www.bioinformatics.org/sms2/

NEBCutter Restriction Enzymes Checker

http://tools.neb.com/NEBcutter2/index.php

Quickchange Mutagenesis Design Tools

http://www.stratagene.com/sdmdesigner/default.aspx

PredictProtein server

http://www.predictprotein.org/

PSIPRED Protein Structure Prediction Server

http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

TarO Target Optimisation Utility

http://www.compbio.dundee.ac.uk/taro/cgi-taro/targpipe_home.pl?logout=true

Prediction of Protein Crystallizability

http://nmr.cabm.rutgers.edu:8080/PXS/

ClustalW EBI server for multiple sequence alignment

http://www.ebi.ac.uk/clustalw/

RONN Prediction of Disorder in Proteins

http://www.strubi.ox.ac.uk/RONN

PrediSi PREDIction of SIgnal peptides

http://www.predisi.de/

OPAL Protein Analysis Tool

http://www.oppf.ox.ac.uk/pn/opal/OPAL.php

SOSUIsignal Signal Sequence Prediction Tool

http://bp.nuap.nagoya-u.ac.jp/sosui/sosuisignal/sosuisignal_submit.html

Buffer Calculator

http://www.liv.ac.uk/buffers/buffercalc.html

Structure Manipulation and Analysis:

DynDom Protein Domain Motion Analysis

http://fizz.cmp.uea.ac.uk/dyndom/

PISA - Protein Interfaces, Surfaces and Assemblies

http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

Autodep PDB Deposition Tool (EBI)

http://www.ebi.ac.uk/msd-srv/autodep4/index.jsp

Universities and Institutions:

University of Pavia

http://www.unipv.it/

Dept. of Biology and Biotechnology

http://dipartimenti.unipv.eu/on-dip/genmic/Home.html

European Molecular Biology Organization

http://www.embo.org/

International Union of Crystallography

http://www.iucr.org/

The Vizier Project

http://www.vizier-europe.org/

Oxygreen Consortium

http://www.rug.nl/oxygreen/index

EMBO Young Investigator Programme

http://www.embo.org/yip/

Italian Association for Cancer Research (AIRC)

http://www.airc.it/

Epigenomics Flagship Project EPIGEN

http://www.epigen.it/

Institute for Advanced Study (IUSS) of the University of Pavia

http://www.iuss.unipv.it/eng/

Am. Chem. Soc. Petroleum Research Fund (ACS-PRF)

http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=prf%5Cindex.html

Fondazione Cariplo - Cariplo Foundation

http://www.fondazionecariplo.it

Synchrotron Light Sources:

ESRF (Grenoble, France)

http://www.esrf.fr/

SLS (Villigen, Switzerland)

http://sls.web.psi.ch/view.php/about/index.html

DESY (Hamburg, Germany)

http://www.desy.de/html/home/index.html

ELETTRA (Trieste, Italy)

http://www.elettra.trieste.it/

CCLRC (Daresbury, United Kingdom)

http://www.srs.ac.uk/srs/

Diamond Light Source (United Kingdom)

http://www.diamond.ac.uk/default.htm

Resources for online PDB displaying:

JMOL Java Applet

http://jmol.sourceforge.net/applet/

MDL Chime (MS Win32 only)

http://www.mdlchime.com/

Rasmol Documentation

http://www.bernstein-plus-sons.com/software/rasmol/doc/rasmol.html

An Introduction to Chime Scripting

http://www.clunet.edu/BioDev/omm/scripting/molmast.htm

JMOL Users Archives

http://sourceforge.net/mailarchive/forum.php?forum=jmol-users

Discontinued web pages from our Website:

Our old Structures Gallery Page

http://www.unipv.it/biocry/structures.php

Our old Crystal Gallery Page

http://www.unipv.it/biocry/crystals.php