Links

Programs

• Collaborative Computational Project No. 4 (CCP4) - crystallographic software suite
• Coot - for model building, model completion and validation
• Swiss-PdbViewer - for viewing and manipulating 3D-structures
• PyMol - also for viewing and manipulating 3D-structures
• Dino - again for viewing and manipulating 3D-structures

Synchrotrons

• The Diamond Light Source in Oxfordshire (UK)
• The EMBL Hamburg Outstation (Germany)
• The European Synchrotron Radiation Facility in Grenoble (France)

Web tools and databases

• Protein Data Bank - repository of 3-D biological macromolecular structure data
• PDBsum - an overview of every macromolecular structure deposited in the PDB
• ExPASy Molecular Biology Server - sequence databases etc.
• PSI-Blast - sequence similarity search tool
• Pfam - Protein families database of sequence alignments
• SCOP - Structural classification of proteins
• CATH - Protein structure classification
• Homstrad - Homologous structure alignment database - also a link to FUGUE
• CPHmodels - homology modeling server
• JPRED2 - secondary structure prediction
• PSIPRED Server - Protein structure prediction server
• Grease - hydropathy plots
• TMHMM Server - prediction of transmembrane helices in proteins
• COILS server - prediction of coiled coil regions in proteins
• Superfamily server - assignment of homology to genome sequences using a library of Hidden Markov Models that represent all proteins of known structure
• Phyre - Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information
• The Meta Server server - submits your sequence to several ab initio structure prediction servers
• The Dali Server - for finding structural homologues
• STAN - the STructure ANalysis server
• EMBOSS - Pairwise Alignment Algorithms
• TCOFFEE - A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, Protein Sequences and Structures
• MultAlin - Multiple sequence alignment
• Chroma - tool for generating annotated multiple sequence alignments in a convenient format for publication
• ESPript - Easy Sequencing in Postscript
• PRODRG2 - will convert coordinates for small molecules in PDB format into a variety of formats
• MolProbity - structure validation
• FoldIndex - predicts whether your sequence will fold
• GlobPlot - explores protein sequences for globularity and disorder
• DisEMBL - Protein disorder prediction
• DISOPRED2 - Disorder Prediction Server
• Web Elements - periodic table info. by Mark Winter

Miscellaneous

• European Macromolecular Crystallographers List (2007)
• Entrez-PubMed

Other biological chemistry project leaders

• Tony Maxwell (Head of Department)
• Stephen Bornemann (Associate Head of Department)
• Janneke Balk
• Mark Banfield
• Dave Evans
• Rob Field
• George Lomonossoff
• Sarah O'Connor

Senior Scientists

• Shirley Fairhurst
• Mike Naldrett