Some Basic Stuff

Biology/biochemistry
 
• The On-Line Biology Book
• The Biology Project
• Introduction to Cell Biology
• The Virtual Biochemistry Laboratory of the Nobel Foundation
• Cells Alive
• Interactive Biochemistry
• Cell Biology Laboratory Manual
• Gluconeogenesis
• Introduction to Glycolysis
• Beta Oxidation of Fatty Acids
• Medical Biochemistry
• Biophysics Textbook On-Line
• BioComputing Hypertext Coursebook
• EMBnet Biocomputing Tutorials
• Internet Tutorial in Biochemistry and Biophysics - Biomolecular Structures
• Molecular Graphics Manifesto
• Primer on Molecular Genetics
• Distant homologies: motifs, patterns, profiles
• Sequence analysis: review@Harvard ; a  Pedestrian guide ; Alignment and Database Scanning ; A Gentle Guide to Multiple Alignment
• Metabolic pathways
• Information Sources on Biological Pathways
• ExPASy - Biochemical Pathways
• WIT - what is there (Argonne)
• EMP Database of Enzymes and Metabolic pathways (Argonne)
• BBID-Biological Biochemical Image Database (NIH)
• BRITE: Biomolecular Relations in Information Transmission and Expression
• Pathways @MIPS
• Glycogen & Glucose
• The University of Minnesota Biocatalysis/Biodegradation Database
• Klotho pathways
• Soybean genome project including clickable pathway maps


  Unix/Linux
 

• the UNIX Reference Desk
• XEmacs User's Manual
• Uppsala Software Factory - Unix for Beginners
• Unix Help for Users and mirrors
• UNIX Shell Script Tutorials & Reference
• Using Unix on Uniform Access Computers
• SHELLdorado
• Unix Shell Scripts
• Tcl and Tk Manual Pages
• An AWK Tutorial
• SUT Scalable UNIX Tools for Clusters
• Linux Newbie
• Linux Applications in Crystallography
• SAL Biocomputing and Linux
• Library of Linux Software
• more linux stuff @ doclib.org
• Debian packages in Biology
• Molecular Biology programs for Linux
• MOKs RPM packages


X-Ray Crystallography
 

• X-Ray Data Booklet (Berkeley)
• Crystallography 101 (Bernard Rupp)
• Refinement Workshop, York
• VSNS-PPS - Virtual School of Natural Sciences: The Principles of Protein Structure
• Space Group Diagrams and Tables
• X-ray Anomalous Scattering and  X-ray Absorption Edges (Washington)
• How to go MAD at CHESS
• The Atomic Scattering Factor Files
• Principles of Protein Structure
• X-ray diffraction data collection (including Optimizing diffraction data collection)
• Randy Read's Protein Crystallography Course
• Processing for Beginners - Data to Density (for molecular replacement)
• X-Ray Diffraction:  Tutorial 1  Tutorial 2 Tutorial 3

Crystallisation

• BioMagResBank (NMR data; Wisconsin)
• Heavy-Atom Databank (heavy-atom derivatives)
• BMCD (crystallisation conditions; NIST)
• Growing Crystals that will make you happy
• Membrane Proteins Crystallisation
• Gitay's Practical guide to cryo-crystallography
• Protein Crystallisation Protocols
• XAct
• XDrop and XFact
• eTray
• XtalMake  (crystallisation  @llnl)
• XtalGrow  (crystallisation  software)

• XDS
• HKL package
• MOSFLM

•  
• CNS
• CCP4
• SHELX
• ARP/wARP
• SnB Shake and Bake
• Solve
• XtalView
• SHARP
• TNT
• EPMR
• COMO
• 
• Manuals
• Uppsala Software Factory - Tutorials
• Making the most of your search model
• Good Model-building and Refinement Practice
• A crystallographer's guide to interpreting WHATIF output
• Taking the fun out of map interpretation ...
• Uppsala Software Factory - OMAC index
• Biomacromolecular speleology
• Dictionaries for Heteros
• Masks made easy
• A super position
• OOPS-a-daisy
• Les amis d'O
• Déjà-vu all over again

• The GIMP
• MOLRAY
• ORTEP-III - Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations
• Spock
• DINO
• Raster3D
• BobScript
• VMD
• MDL Information Systems (Chime & ISIS/Draw)
• MSMS
• GRASP
• Molecules R US (NIH)
• SWISS-3DIMAGE (ExPASy)
• Deep View Swiss-PdbViewer (ExPASy)
• Swiss-Pdb Viewer(ExPASy)
• IMB -Jena (Image Library of Biological Macromolecules)
• Biochemistry Graphics on the Web (CMU)
• GRASS (Graphical Representation and Analysis of Structure Server; Columbia)
• STING (Sequence To and withIN Graphics; Columbia)
• Molecular Graphcis Art Shows (Scripps)
• MolVisIndex (World Index of Molecular Visualization Resources)
• Freely available molecular visualisation programs
• Graphics and Visualisation (Torino)
• Rasmol (Bernstein)
• Rasmol (UMass)
• Chime (MDL)
• MolScript (Kraulis)
• Molscript - colour names
• MolMol (ETH)
• Mage (Duke)
• Protein Explorer (UMass)
• Roadmap -  surface display
• WebLab Viewer Lite (Accelrys)
• WebMol ( EMBL, Heidelberg)
• PyMOL
• LIGPLOT (UCL)
• Garlic (Croatia)
• Biomolecular Morphing (Tutorial@USF)

• 
• Superintendent  (Uppsala Structure Police) tutorials
• Validation papers
• Model Validation
• Sructural Databases
• Motif Recognitation
• Model Quality
• Model Building
• Structure prediction
• Structure Recognitation
• MOLEMAN2 server
• EDS (Electron Density Server)
• DDQ (Difference Density Quality)
• PARVATI Validation and Analysis Tool for atomic or near-atomic resolution  (Washington)
• PROCHECK
• DomainFinder
• EDPDB
• SURFNET
• WHATIF
• WHAT IF servers
• PDBReport
• Biotech validation server Validation Suite for Protein Structures (EBI, UK)
• Biotech validation server Validation  Suite for Protein Structures (EMBL-Heidelberg, Germany))
• ERRAT server   Structure Evaluation Server (UCLA, US)
• Verify3D server  Another Structure Evaluation Server@UCLA
• ANOLEA server (Atomic Non-Local Environment Assessment; Namur)
• A Glossary of Terms  ( for judging the quality of your model)
• Crystal Twinning server (@UCLA)

 
• EBI-MSD


• Protein DataBank (PDB): <search>
 
• Detailed transition plans to Rutgers University
• Documentation and Information
• ftp to PDB (archives)
• How to link to a specific PDB entry
• Obsolete PDB entries (very useful!!)
• PDB Select (Representative group of high resolution crystal structures)
• Processing status of entries 'ON HOLD'
• Search Lite (easy search of PDB entries)
• Submit data to PDB (AutoDep Input Tool)
• Validation server (AdIt)
• Protein Data Bank@NIST
• Protein Data Bank @EBI
• PDB current holdings


Interfaces to structural databases
 

• PDBsum (UCL)
• PDBFINDER (CMBI)
• 3DB Browser (EBI)
• PDB Lite (EBI)
• PDBLite
• MMDB (NCBI)
• Entrez-Structure (NCBI)
• PDB Lite
• OCA (Weizmann)
• BioMolQuest (Danforth Center)
• PDB at a Glance (NIH)

• SAS (Sequences Annotated by Structure; UCL)
• Enzyme Structures Database (UCL)
• Atlas of Protein side-chain interactions (UCL)
• Side-chain and main-chain hydrogen bonding (UCL)
• LPFC (core-structure database; Stanford)
• ASTRAL (compendium for sequence and structure analysis; Stanford)
• 3Dee (database of protein-domain definitions; EBI)
• 3Dseq (correspondence between SWISS-PROT and PDB protein sequences; EBI)
• PQS (quaternary structures of PDB entries; EBI)
• PRINTS -Protein Fingerprints Database
• PRODOM Protein Domain Database
• MolMovDB (Database of Macromolecular Movements, Yale)
• PROMISE (Prosthetic groups and Metal Ions in Protein Active Sites Database; Leeds)
• SPIN-PP (Protein-protein interfaces; Columbia)
• MutaProt (structural effects of point-mutations; Weizmann)
• ProDDO (disorder in proteins; Tokyo)
• Protein Hydrophilicity/Hydrophobicity Search and Comparison Server
• Connolly surface
• SLoop (database of super secondary fragments; Cambridge)
• BIND Biomolecular Interaction Network Database
• Interact - A Protein-Protein Interaction database (Manchester)
• MINT Protein interactions database @CBM, Rome
• DIP (Database of Interacting Proteins)

Databases for specific protein families

• PKR (Protein Kinase Resource; SDSC)
• Antibodies - Structure and Sequence (Martin)
• Membrane lipids
• AAA (ATPases Associated with various cellular Activities)
• Glucoamylases
• Membrane Poteins
• MDB (Metalloproteins; Scripps)
• HIVdb (HIV proteases; NCI)
• Prolysis (Proteases and protease inhibitors; Tours)
• CAZy (Carbohydrate Active Enzymes; CNRS)
• Chaperonins
• TIM-DB (TIM-barrel domains; Tarragona)
• Lipocalin Web Site (Jenner)
• ESTHER (alpha/beta hydrolases homologous to cholinesterases; INRA)
• NucleaRDB (database of nuclear receptors; UCSF)
• Glucocorticoid receptors
• Thyroid hormone receptor
• GPCRDB (G-protein coupled receptors; CMBI)
• EF-hand calcium-binding proteins data library (Vanderbilt)
• Serine Proteases (St Louis)

• CATH(classification database; UCL)
• SSAP server (superimposing two structures; UCL)
• PROCAT (UCL)
• SCOP (classification database; MRC-LMB)


• FSSP (Fold classification based on Structure-Structure alignment of Proteins)
• TOPS - protein topology database and server
• DALI similarity server
• DBAli, DataBase of sequence and structure Alignments
• PALI, Phylogeny and ALIgnment of homologous protein structures
• DEJAVU similarity server (Uppsala)
• SPASM server (Uppsala)
• CE similarity database and server (SDSC)
• VAST similarity database and server (NCBI)
• Guoguang Lu's programs and servers (Lund)
• MATRAS server (Japan)
• STRUCTAL server (superimposing two structures; Yale)
• K2 server (superimposing two structures; Boston)
• PROSUP server (superimposing two structures; Salzburg)
• MetaMeme (Motif hidden Markov modeling of biological sequences)
• DSMP (Database of Structural Motifs in Proteins; CDFD, India)
• Site Database (Jena)
• Protein-Protein Interaction Server

• Protein Structure Prediction Center
• ModBase
• Structure Prediction Meta-Server (France)
• PredictProtein
• Jpred2
• PROTEIN DOMAIN SERVER
• PREDATOR, STRIDE, ORPHEUS & PEDANT
• BMERC's PSA Server
• Servers @ University of Cambridge


Prediction of Transmembrane Regions and Membrane Protein Topology
 

• TMAP Karolinska Institute
• TMHMM (DTU Technical University of Denmark)
• PredictProtein (EMBL, Heidelberg)
• TMAP (EMBL, Heidelberg)


Protein Modelling and Threading
 

• FRSVR (threading; UCLA)
• SAM-T99 (threading; UCSC)
• 3D-PSSM (threading; ICRF)
• 123D+ (threading; NCI)
• SWISS-MODEL (ExPASy)
• CPHmodels
• Homology modelling for beginners
• Computational Chemistry Exhibition
• FOLD-X (calculate folding pathway or stability of mutant structures; EMBL, Heidelberg)
• Network Sciences: Molecular Surfaces
• HSSP (database of homology-derived protein structures; EBI)
• SuperStar - Prediction of protein binding-site interactions (Cambridge)
• Resources in Molecular Modelling

• ReLiBase (REceptor-LIgand interaction dataBASE; EBI)
• LIGAND <search> Database of Chemical Compounds and Reactions in Biological Pathways
• RELIWE - Calculation and Prediction of Receptor Ligand Interactions
• HIC-Up (USF)
• HetSEL   (USF; SBNet)
• Hetero Components Database (Jena)
• Klotho (Biochemical Compounds Declarative Database; St. Louis)
• MathMol (Library of 3-D Molecular Structures; New York)
• ACA SMALL MOLECULE SIG
• CSD (Cambridge Crystallographic Data Centre ) & documentation

    ExPASy Molecular Biology Server
• ExPASy Homepage
• SWISS-PROT
• PROSITE
• Tools at ExPASy
  National Center for Biotechnology Information
• NCBI Homepage
• BLAST
• BLAST information guide
• Entrez
• GenBank
• ORF Finder (Open Reading Frame Finder)
• EMBL @Heidelberg
• SRS5 (EMBL Heidelberg)
• Pmotif  protein motifs in DNA (Virtual Genome Center, Minnesota)


• EBI  Homepage
• SRS6
• Blitz
• FASTA
• InterPro - sequence pattern search combining PROSITE, PRINTS, SMART, etc .
• Tools at EBI
• ProSAL (Protein Sequence-Analysis Launcher; USF)
• BLOCKS  (biological sequence analysis; Seattle)
•  eMOTIFS (Stanford)
• PIR (Georgetown)
• META PP (Columbia)
• ProDom (Toulouse)
• BIORES resources in sequence analysis (Nottingham)
• BALLAST: BLAST post-processing based on locally conserved segments (Strasbourg)
• HMMER - Biological sequence analysis using profile hidden Markov models (St Louis)
• The Exon-Intron Database (Harvard)
• BCM Search Launcher: General Protein Sequence/Pattern Searches@ Baylor, HGSC
• InBase, The New England Biolabs Intein Database

• DiAlign2 (Genomatix)
• PHYLIP (Washington)
• PIMA (BCM)
• ClustalW (EBI)
• AMAS - Analyse Multiply Aligned Sequences (EBI)
• ClustalW (EMBL, Heidelberg)
• CLUSTALW (NPS)
• Clustal X (Strasbourg)
• DbClustal (Strasbourg)
• MSA (Michigan)
• Ctree, CLustalW and MSA (Michigan)
• Match-Box
• ClustalW, CAP, MAP, PIMA, MSA, Block Maker, MEME, Match-Box (BCM)
• Block Maker
• MULTALIN
• MultAlin
• FarOut (Uppsala)

Related

• Glycoscience network
• CARBHYD - Carbohydrate Information (Iwoa)
• N-Glycan Structure and Biosynthesis (Mainz)
• Glycobiology Page @The University of Alberta
• Proteoglycan/glycosaminoglycan Home page
• Complex Carbohydrate Research Center  @University of Georgia
• Sugabase, a database of Carbohydrate NMR structures
• Mizutani Foundation for Glycoscience
• SWEET 3D models of saccharides from their sequences

Literature

• to be published references in PDB entries
• IUCR ( Crystallography Journals online)
• Theoretical and Mathematical Biology Journals
• HighWire (Stanford)
• PubMed
• WebMedLit
• BioMed Central
• PubMed Central
• PubMed Express
• PubSCIENCE
• ISI
• BioMedNet
• National Center for Biotechnology Information (NIH)
• PNAS Proccedings of the National Academy of Sciences (US)
• Scirus (scientific information searches)
• PubCrawler
• Bioinformatics
• Ergito  (Life Science modules)

• TIGR Microbial Genome Database
• GeneSensus @Yale
• BioKnowledge - Genome databases (Proteome)
• OMIM  catalog of human genes and genetic disorders (NCBI)
• GenomeNet ( see also KEGG - Kyoto Encyclopedia of Genes and Genomes)
• MAGPIE Automated Genome Project  Investigation Environment (Rockefeller)
• HGVBase (Human Genome Variation database)
• GeneLynx
• D-aminos - List of putative real D-amino acid residues in the PDB
• EMBOSS - The European Molecular Biology Open Software Suite
• BiowURLd (EBI)
• INFOBIOGEN - The Catalogue of Databases
• DEAMBULUM - BIO NETosphere thematic exploration (biology, biocomputing, etc..)
• The Protein Sidechain Webpage
• Protein Topology Home Page (EBI)
• ICM ( Peptide prediction, homology modeling,graphics loop simulations, etc. @Oulu)
• Insight II
• TRITON
• DOCK
• MODELLER
• VEGA
• BIORES (UK gateway to internet resources in biological& biomedical research)
• Namot (Nucleic Acid Modeling Tool)
• NAB (Nucleic Acid Builder)
• Resources for Macromolecular Structure Information (Brussels)
• Structure-related resources (York)


• Conferences
• Courses
• BioSEL (Bio Search-Engine Launcher; Uppsala)
• ProSAL - Protein Sequence Analysis Launcher, Uppsala
• BRENDA
• Protein Structure web site
• Structures of amino-acid repeats
• Proteome analysis
• GETAREA (Solvent-accessible surfaces)
• Cutter (proteolysis)
•   Dombo Journal