Miscellaneous Web Sites

Web Catalogues and search engines

Alta Vista - Search engine
Biomolecular Engineering & Structural Biology - European resources
Electric Monk - Search engine
E-mail address finder - Search engine
Excite - Search engine
Google - Search engine
HotBot - Search engine
Open Text - Search engine
Infoseek - Search engine
Inktomi - Search engine
Mamma - The Mother of all Search Engines
METACRAWLER
Power-Search - Search engine
Search Engine Sizes - Search Engine Watch
Search Voyeur - Search requests submitted to WebCrawler (Java version)
W3 Search Engines - Home page searcher (Oxford site)
UK Guide - The UK and Ireland - an active map
UK WWW servers - UK list of WWW servers
WebCrawler - WebCrawler database
WWW Subject Catalogue
Top 100 Web sites

Protein-related Databases

ANOLEA - A WWW server to assess protein structures
AutoDep/WHATIF notes - Gerard Kleywegt's help document

Backbone-Dependent Rotamer Library - Roland L. Dunbrack
Bioinformatics Resources - Bloomsbury Centre for Structural Biology
Bioinformatics Tools - Virtual course in Bioinformatics tools, using Java
Biolinks - Search engine for Biological information
BioMagResBank - Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids
Biomolecular Morphing - Visualising structural differences between molecules
BioShoW UK - UK bioinformatics resources.
Biotech Validation - Protein structure validation server (EBI mirror)
Bio-wURLd - URL's related to bioinformatics, biochemistry, and molecular biology.
BUBL

CASP - Critical Assessment of Methods for Structure Prediction, at the Protein Structure Prediction Center
Chaperonins - The Chaperonin Home Page
Cholinesterases - Cholinesterases
CMC Modelling Guide - CMC group at Utrecht University
CMS - Compendium of resources for Molecular Biology, Biotechnology, etc. (SDSC)
Colipage - database of E. coli paralogous genes
Crystallographic refinement and rebuilding - Gerard Kleywegt
CSD - Cambridge Structural Database
CSD - Documentation

D-aminos - List of putative real D-amino acid residues in the PDB
Datasets - Roland Dunbrack's culled PDB datasets
DDBASE - Domain boundaries database
3D-PSSM - Fold recognition
DSSP - Secondary structure database
DSMP - Dictionary of Structural Motifs in Proteins

EMBOSS - The European Molecular Biology Open Software Suite
Entrez - The NCBI WWW Entrez Browser
Enzyme - Enzyme nomenclature database
Ergito - Life Science modules
European Macromolecular Crystallographers List
FPAT - Regular expression searches of sequence databases
FSSP - Fold classification based on Structure-Structure alignment of Proteins

GCRDb - The G-protein coupled receptor database
GENIUS - ORFs -> 3D protein structures

HETERO - All hetero groups in the PDB (consisting of a single file in PDB format)
HGMD - Human Gene Mutation Database, Institute of Medical Genetics in Cardiff
HIC-Up - Hetero-compound Information Centre, Uppsala
HIV proteinases - Database of 3D structures at NIH
HOMSTRAD - Homologous Structure Alignment Database
HOVERGEN - Homologous Vertebrate Genes Data Base
Hydrogen atom names - Conventions in different systems

Iditis - Personal Iditis Demo
Image Library of Biological Macromolecules - Jena, Germany
INFOBIOGEN - The Catalogue of Databases
InterPro - sequence pattern search combining PROSITE, PRINTS, SMART, etc
Isostar - Local access
IUPAC recommendations - International Union of Pure and Applied Chemistry

JaMBW - Java-based Molecular Biology Workbench
JOY - JOY output for single proteins or multiple sequence alignments

Kinases - SDSC Protein Kinase Database Project

LIGAND - Database at GenomeNet, Japan
LPFC - Library of Protein Family Cores

MAPS - an automated program for Multiple Alignment of Protein Structures
MDB - Metalloprotein site Database and Browser
MODBASE - Database of Comparative Protein Structure Models
Molecular Graphics and Modelling Society
MOOSE - Macromolecular Structure Query
MSD - Macromolecular Structure DataBase Group at the EBI

NDB - Rutgers Nucleic Acid Database

OLDERADO - On Line Database of Ensemble Representatives And DOmains
OMIM - Online Mendelian Inheritance in Man

PDB - Research Collaboratory for Structural Bioinformatics (RCSB)
PDB file format - Version 2.0, February 21, 1996
PDBobs - Archive of obsolete PDB entries
3DBbrowse - Brookhaven Protein Data Bank browser
PDBfinder - PDB Finder database (EMBL)
PDBsum - Summaries and structural analyses of PDB data files (UCL)
PDBsum - Summaries and structural analyses of PDB data files (Birkbeck mirror)
Pedro's research tools (Swiss site)
Pedro's research tools (German site)
Pedro's research tools (US site)
Pfam database of protein family alignments and HMMs
PRINTS - Protein motif fingerprints
Proceedings of Crystallographic Computing 7 - Computing Commission of the IUCr
ProDom - Protein domain database
PROLYSIS - Database of proteases and protease inhibitors
PROMISE - Prosthetic centres and metal ions in protein active sites
PROSITE - Dictionary of protein sites and patterns
ProStar - The Protein Potential Site
Protease Inhibitors - What They Are, How They Work, When to Use Them
Protein Motions Database - at Stanford
ProtoMap - hierarchical classification of SWISSPROT
PSORT - Prediction of protein localized sites

QuickPDB - A Sequence/Structure Search and Display Java Applet

Ramachandran revisited - Gerard Kleywegt
ReliBase - Receptor/Ligand complexes
RELIWE - Calculation and Prediction of Receptor Ligand Interactions
Resources for Macromolecular Structure Information - List of major resources for Macromolecular Structure

Sacch3D - Structural Information for Yeast Proteins
SCOP - Structural classification of proteins
SMILES - Simplified Molecular Input Line Entry Specification
Sound Of Sequence - Mapping of amino acids to musical notes
SRS - Network Browser for Databanks in Molecular Biology
SAVS - Structure Analysis and Verification Server
SWISS-PROT - Annotated protein sequence database
SYQUA - Bioinformatics Web Site

TMpred - Prediction of Transmembrane Regions and Orientation
TOP - Protein structure comparison
TOPS - Protein topology cartoons

UCLA Fold Recognition Server - Structure Prediction Server
University of York - EEC structure validation
Uppsala C-alpha Ramachandran Server
Uppsala Electron Density Server - Electron density maps viewed in VRML
Uppsala Electron Density Server - Old version

Verify3D - UCLA Structure Evaluation Server
Virtual Biology - Animations of cell processes
VSNS-PPS - Virtual School of Natural Sciences: The Principles of Protein Structure

WebMol - Java PDB Viewer
WIT - What Is There: database of metabolic pathways
World Database of Crystallographers

Human Genome

HGSI - Human Genome Sequencing Index Tables
HGMD - Human Gene Mutation Database, Institute of Medical Genetics in Cardiff
HGVbase - HGVbase (Human Genome Variation database)
Human genome sequencing data - Weizmann Institute
Human Genome Sequencing Status - Sanger Centre
MOT - Genome Monitoring Table, EBI
GAC - Genome Annotation Consortium
The Genome Channel - Sequencing progress
HSM - Human Sequence Map Index
TSC - The SNP Consortium Ltd
Working Draft - University of California, Santa Cruz

Other Genomes

The Fish Net - An access to Zebrafish Research Databases
GenBank - GenBank search at the NCBI
GeneQuiz - Genome analyses
GOLD - Genomes On Line Database, 1.0
KEGG - Kyoto Encyclopedia of Genes and Genomes
KMeyeDB - Keio Mutation Database for eye disease genes
TIGR - Database of Microbial Genomes

Journals

Acta Crystallographica Section D
Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
BioMedNet - Access to Biological and Medical Journals
BIDS ISI
Bioinformatics
CCP11 Newsletter
Chemistry & Biology
ChemWeb
Current Biology
Current Opinion in Structural Biology
Current Opinions (free until 31 Dec 99)
Evaluated MEDLINE
HMS Beagle - A BioMedNet publication
IDEAL - International Digital Electronic Access Library
ingentaJournals (Bids password)
inScight - Daily Science News
Journal Abbreviations - NCBI's Pubmed
JASJournal Abbreviation Sources -
Journal of Applied Crystallography
Journal of Computer-Aided Molecular Design
Journal of Computational Chemistry
Journal of Molecular Biology
Journal of Molecular Modeling
Journal of Molecular Recognition
Macromolecular Structures
MIMAS Web of Science
MIT Biology Hypertextbook
Network Science
Nucleic Acids Research
Free Medical journals
PubMed - National Library of Medicine's database of Medline citations
Nature
Nature Structural Biology
New Scientist
PNAS - Proceedings of the National Academy of Sciences, USA
Protein Engineering
Protein Science
Proteins: Structure, Function and Genetics
Science
Scientific American
Structure
Others
UCL Library e-journal links
The Web of Science

Software

AutoDock - Automated docking of flexible ligands to macromolecules
AQUA - Analyzing the QUAlity of NMR structures
BALL - Biochemical Algorithms Library
BobScript - Robert Esnouf's extensions to MolScript version 1.4
CAD - Structural comparison program using residue contact surface areas
Chem Tutor - Free downloadable NMR tutorial
CCP4 - The CCP4 Program Suite
ChemX - Chemical Design
Chime - Molecular Visualization program
Cn3D - Entrez's molecular Visualization program
Crystallography Software
Crystal Office 96 - Atomic Softek
Geometry - Directory of Computational Geometry Software
GSL - GNU Scientific Library
DOCK - Kuntz group, UCSF
DSSP - Kabsch & Sander
FlexX - Prediction of receptor-ligand interactions
FTDOCK - Fourier Transform DOCKing
GAMS - Guide to Available Mathematical Software
GIMP - Graphics Manipulation Program
Graphics Software - (at Yahoo)
GRASP - Graphical Representation and Analysis of Structural Properties
HMMER - Biological sequence analysis using profile hidden Markov models (HMMs)
ImageMagick - image-display under Xwindows
Kinemage - Kinemage Home Page
LEDA - Library of the data types and algorithms of combinatorial computing
Math Archives - Public domain algorithms
MS Kermit - file transfer software
mmCIF Software Tools - from NDB at Rutgers
mmCIF Dictionary, DDL and software - (EBI mirror)
Molecular Biology Software List - Miscellaneous
Molecular Modeling Software List - NIH Molecular Modeling site
MOLMOL - Biomolecular graphics/analysis package
MSI - Molecular Simulations Inc.
MolScript - Molecular graphics as PostScript plots
NAOMI - 3D structure analysis of proteins
NETLIB - Publicly available algorithms
Numerical Recipes
O - Protein crystallographic package
ORTEP-III - Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations
ORTEP-3 for Windows - Windows version of ORTEP-III
PASS (Putative Active Sites with Spheres) - Including Calculation of Volumes and Surfaces
Protein packing - Including Calculation of Volumes and Surfaces
Protein Explorer - Eric Martz's RasMol-like interface for Chime
PyMol - Open-source molecular graphics program under Python
RasMol development - Bernstein + Sons
RasMol Home Page - Molecular Visualisation Program
RasMol Manual - Molecular Visualisation Program
Raster3D - 3D Molecular Rendering (Local documentation)
Rayshade - System for creating ray-traced images
Ribbons - General molecular illustration and error analysis in protein crystallography
Roadmap - Display of surface of a macromolecule, and its properties
RSRef - Refinement of an atomic model into electron density
Scientific Applications on Linux - SAL
Scientific Software - (at Yahoo)
Shockwave
SIMPLEPLOT - Graphics software
SWISS_PDBViewer - Molecular Visualisation Program
SYBYL - Molecular modelling
SuperStar - Prediction of protein binding-site interactions
XtalView - X-ray crystal structure solution
Visualize - Molecular Visualisation Program
WHAT_CHECK - Validation of protein and nucleic acid models
WPDB - PC-based Macromolecular Structure Interrogation
X-PLOR - A System for X-ray Crystallography and NMR
XtalView - X-ray crystal structure solution

Universities & Laboratories

Birkbeck College - Department of Crystallography
University of Birmingham
EBI, Hinxton - European Bioinformatics Institute
EMBL, Hamburg - European Molecular Biology Laboratory
EMBL, Heidelberg - European Molecular Biology Laboratory
MRC Clinical Sciences Centre - Imperial College School of Medicine at Hammersmith Hospital
University of York

Museums, etc.

British Library - OPAC97, Online Public Access Catalogue
Greenwich2000
Hadrian's Wall
Hampton Court Palace - and Real Tennis
Index of science-related Museums -
Leeds Castle, Maidstone
Llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogoch - The village with the longest name in Britain
Natural History Museum - Index
Natural History Museum - Current Exhibitions
The Patent Office
Science Museum -
Stonehenge - Stonehenge 3D model using Viscape
Stone Pages - Stones of England, Scotland and Ireland
World Heritage List

Weather

UK Met. Office - Weather charts
Wunderground - Worldwide weather forecasts
Weather movie - National Technical University of Athens
NJO 5-day Weather forecast - London
NJO 5-day Weather forecast - Warsaw

Sports

Newspapers & Magazines

Daily Telegraph
Evening Standard
The Guardian
GO2 - The Guardian OnLine on-line
The Independent
PA NewsCentre - The Press Association on-line (vidiprinter / what the papers say)
Monster Magazine List - The Electronic Newsstand
Private Eye
Radio Times - TV guide
THESIS - Times Higher Education Supplement Internet Service
The Times

Maps

Transport

General science

C/C++ - About.com Guide
Chemistry - About.com Guide
Mathematics - About.com Guide
Physics - About.com Guide
PSIgate - Physical Sciences Information Gateway

Astronomy

Astronomy Picture of the Day - NASA
Comet Hale-Bopp - The Great Comet of 1997
Mars Pathfinder - Jet Propulsion Laboratory
NASA - Jet Propulsion Laboratory
The Nine Planets - and their moons

Literature

Bibliomania - On-line fiction and non-fiction
First Lines - Quiz
English and it History - Old and Middle English
Literary resources on the Net - English and American literature
Old English Pages - Including sound files
Pride and Prejudice (annotated) - Jane Austen

The Bookshop

Primrose Hill Books

Archaeology and Classics

Ancient World Web - Indexes of archaeological sites
Classics links - Classics and Mediterranean archaeology
Current Archaeology
Duke Papyrus Archive - Texts and images of papyri from ancient Egypt
Mark Millmore's Ancient Egyptian Page - Pyramids, Temples, Kings and Queens, etc
Theban Mapping Project - Theban Necropolis, Valley of the Kings, KV5, Egyptology