Links for Protein Crystallography, Sequence Analysis and Mathematics

QuickLinks:
Protein Crystallography
Synchrotrons

Databases

Software

Sequence Data & Analysis
Sequence searches

Motif searches

Sequence alignment

Miscellaneous

Mathematics

Protein Crystallography

Synchrotrons

This list only contains synchrotrons that people in our lab are likely to visit.

ALS: Macromolecular Crystallography Facility at the Advanced Light Source
Argonne: Argonne Advanced Photon Source (APS);
Structural Biology Center
IMCA-CAT (Industrial Macromolecular Crystallography Association)
Daresbury: Daresbury Laboratory links to stations 7.2, 9.5 & 9.6
DESY: Hasylab (Hamburg Synchrotron Laboratory)
ELETTRA: Trieste synchrotron Beamline 5.2 R X-Ray Diffraction
ESRF: European Synchrotron Radiation Facility
Beamline ID2 (High brilliance Biocrystallography)
Beamline BM2 (Macromolecular crystallography - French)
Beamline ID14A,B (Macromolecular crystallography)
Beamline BM14/BL19 (optimized for MAD/SAD experiments)
NSLS: National Synchrotron Light Source (Brookhaven).
Beamline X4A (HHMI multiwavelength anomalous diffraction)
Beamline X4C (HHMI Macromolecular diffraction)
Beamline X12B (Macromolecular static and time-resolved diffraction)
Beamline X12C (Protein crystallography more info)
Beamline X26C (Laue)
SSRL: Stanford Synchrotron Radiation Laboratory (not very informative)

Structure databases

PDB: WWW-entry into the Hinxton PDB mirror (PDB)
SDSC PDB mirror: PDB searches and coordinate retrieval with full text search
BMCD: The Biological Macromolecule Crystallization Database
SCOP: Structural Classification of Proteins
FSSP: Database of Families of Structurally Similar Proteins. (Help
TOPS: Structure-structure homology search (CATH oriented)
WWWTOP: Structure-structure homology search (SCOP oriented)
CATH: Database of Families of Structurally Similar Proteins, used by THREADER
DALI: Database and web tools to analyse structural homologs of a protein
PDBsum: Summary of PDB entries including PROCHECK and PROMOTIF data
ProtMotDB: Database of protein motions, hinge bending, shear, loop flips etc.
Macromolecular assembly database: The "EBI" oligomeric states of proteins database
Rotamers: The Protein Sidechain Webpage, library of rotamer preferences

Protein Crystallography Software

CCP4: CCP4 Program Suite. For documentation click here
ARP/wARP: The Automated Refinement Procedure programs
X-PLOR home page: Includes the the online manual
SHARP/BUSTER: Home page for the Bricogne laboratory
Uppsala Software Factory: Software, Resources and Manuals local copy
TNT: TNT Macromolecular Refinement Package
DENZO/HKL: Home pages of DENZO and HKL software
MaxSprout: Generating protein backbone and side chain atoms from Calpha model
Twinning: Todd Yeates crystal twinning server
HIC-UP: Data-base plus tools to create hetero compound topology files

Sequence Data & Analysis

BLAST: Sequence homology search with the BLAST program. HELP
BLITZ: Sequence homology search with the BLITZ program (only SwissProt) HELP
dbEST: Searching the Expressed Sequence Tags database (often unpublished cDNA's)
FASTA 3.2: Fancy protein<-->DNA sequence search allowing gaps etc. Also allows searches with N-term sequences from peptide mixtures
Find by name etc.

Entrez
Search for proteins/genes based on name, author, organism etc.
SBASE
Sequence dataBASE with additional information and clustering of sequence families
OWL
Search for proteins based on name, author, organism etc.
SWISS
Search for proteins based on name, author, organism etc. (in SwissProt database)
Entrez: Search for proteins/genes based on name, author, organism etc.
SBASE: Sequence dataBASE with additional information and clustering of sequence families
OWL: Search for proteins based on name, author, organism etc.
SWISS: Search for proteins based on name, author, organism etc. (in SwissProt database)
Find motifs

PROSITE
Sequence search for motifs (glycosylation, phosphorylation etc.) HELP. For real scan try ProfileScan
PFAM
HMM-based grouping of protein families
THREADER
Threading with David Jones's THREADER program
ISREC
ISREC-based profile database
PSORT
Predicting Protein Sorting based on sequence and species
BLOCK SEARCH
Sequence search for conserved blocks, gapless multiple aligned sequences. It is good at detecting distant similarities to other protein families. HELP
PROSITE: Sequence search for motifs (glycosylation, phosphorylation etc.) HELP. For real scan try ProfileScan
PFAM: HMM-based grouping of protein families
THREADER: Threading with David Jones's THREADER program
ISREC: ISREC-based profile database
PSORT: Predicting Protein Sorting based on sequence and species
BLOCK SEARCH: Sequence search for conserved blocks, gapless multiple aligned sequences. It is good at detecting distant similarities to other protein families. HELP
Multiple sequence alignment

BLOCK MAKER
Search for conserved blocks in a set of user-given sequences. Is good at detecting distant homologies. HELP
AllAll
Multiple Sequence alignment and derived info (trees, prediction of exposed/buried/loop, prediction of most probable ancestral sequence) HELP
MSA
Multiple Sequence alignment (max 8 sequences)
PredictProtein/PHD
Predict secondary structure, accessibilities, structural homologues etc based on a sequence or multiple sequence alignment
Jpred
A consensus method for protein secondary structure prediction (Barton lab)
ProtEST
Automated search for EST contigs(Barton lab)
EMBL
EMBL computational services
BLOCK MAKER: Search for conserved blocks in a set of user-given sequences. Is good at detecting distant homologies. HELP
AllAll: Multiple Sequence alignment and derived info (trees, prediction of exposed/buried/loop, prediction of most probable ancestral sequence) HELP
MSA: Multiple Sequence alignment (max 8 sequences)
PredictProtein/PHD: Predict secondary structure, accessibilities, structural homologues etc based on a sequence or multiple sequence alignment
Jpred: A consensus method for protein secondary structure prediction (Barton lab)
ProtEST: Automated search for EST contigs(Barton lab)
EMBL: EMBL computational services
Sequence Miscelaneous

pI/Mw
Given a sequence this tool returns the predicted pI & Mw.
amino acids
properties and pictures of the amino acids
families
Database of pre-aligned sequence families.
Yale server
Automated structural alignment server
HOVERGEN
HOmologous VERtebrate GENes, prealigned sequence families
Protomap
An exhaustive hierarchical classification of all proteins in SWISSPROT
DNA -> Protein
Form to convert DNA to protein sequence using 6-frame translation.
TIGR
Database of concatenated Genbank & EST sequences
Flybase
Database of Drosophila Genome FlyBase (UK mirror) FlyBase (US mirror) FlyBase (Japan mirror)
Tutorial
Another Sequence alingment tutorial
Expasy
Pointers to all the tools on the EXPASY server
PairWise & SearchWise
Frameshift aware alignments
HMMER package
Hidden Markov model based profile searches
Pedro
Pedro's BioMolecular Research Tools (very useful)
BIOCAT
EBI's BioCatalog
MVIEW
web site to convert BLAST output into multiple sequence alignment
PSORT
Analyzing and Predicting Protein Sorting Signals
GAPSF
Geometric Aspects of Protein Structure and Function
ProtVal
Protein Structure Validation
PENCE
Protein Engineering Network of Centres of Excellence
pI/Mw: Given a sequence this tool returns the predicted pI & Mw.
amino acids: properties and pictures of the amino acids
families: Database of pre-aligned sequence families.
Yale server: Automated structural alignment server
HOVERGEN: HOmologous VERtebrate GENes, prealigned sequence families
Protomap: An exhaustive hierarchical classification of all proteins in SWISSPROT
DNA -> Protein: Form to convert DNA to protein sequence using 6-frame translation.
TIGR: Database of concatenated Genbank & EST sequences
Flybase: Database of Drosophila Genome FlyBase (UK mirror) FlyBase (US mirror) FlyBase (Japan mirror)
Tutorial: Another Sequence alingment tutorial
Expasy: Pointers to all the tools on the EXPASY server
PairWise & SearchWise: Frameshift aware alignments
HMMER package: Hidden Markov model based profile searches
Pedro: Pedro's BioMolecular Research Tools (very useful)
BIOCAT: EBI's BioCatalog
MVIEW: web site to convert BLAST output into multiple sequence alignment
PSORT: Analyzing and Predicting Protein Sorting Signals
GAPSF: Geometric Aspects of Protein Structure and Function
ProtVal: Protein Structure Validation
PENCE: Protein Engineering Network of Centres of Excellence

Mathematics

GAMS: Guide to Available Mathematical Software (Great!)
Mathematics Information Servers: General info and links to other sites
StatLib Index: Collection of software for a diversity of statistical problems