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SOARING BEAR Ph.D. Pharmacology
index
Scientific advisor to the health professions & herbal industry
index

Biochemistry and molecular biology - large molecules and metabolic pathways

Education & Course: BergStryerNLM - biochem course with structures (Sears, UCSB) - outline (Feig, IU) - Feig - CentroBiolSyst - biopendium proteomics - Bruist USciPhila - Campbell NovaSEU - biochemweb - BlaberFlaStU - McClureCMU - CMU - King IndianaStU - Pearson UVa - biochem (King IndSt) - Microbiotext(Wisc) - medlinetexts - protDNAstrumovies - protfoldanim - protfoldanim - nigms chem of health - BioFarabee - BioEdBaylor - YasaraGraphics - Robertus(UTx) - 462(Az) - Garrett&Grisham - Garrett&Grisham - SynthGenVentnerChurch09 - nakedScientists - HSbioinf - HSbioinf - BioinformaticsCurriculumSearls - textTalwar -
Evolution: darwin -
Calculations: SolutionsThermodyn - dGexamples - Kwiatkowski - kinetics - Calculus122 -

STRUCTURE of large Molecules
proteomePSD - HumanProteinRefDB - HumProteomicsInitiativeExpasy - HumMitochondriaNIST - MSproteomesoftware - BALLalgorithms - BALLalgorithms -

PROTEIN Brookhaven PDB xray coordinates (24k, 7k unique, 5k human): (viewers on compchem page)
PDB rcsb link format: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1K9G - MolToGo (MolRUs)search  link: http://molbio.info.nih.gov/cgi-bin/moldraw?1BR5 - BNL gopher - BNL iris gopher - nih search NRL3d (gdb) - wwpdb - embl srs - nih search - NCBI - UMass - explorer - UCL - bchs pdb list - pdb IDs - bnl pdbBrowse - PDBSum - 1600 Enzyme pdb's Walsh pdb list - pdbselect by homology - zurich list - expasy pdb gifs- EBI - MembranePDB - MembraneProteins - MetaTM - unige search? - unige pending? - yeast proteins - Suehnel protein views: stick, ribbon, cpk - amino acids - metalloprotein (scripps) - metalloprotein - jena - isostar search - 2k non-redundant complexed PDB (Didier) - quaternary structures of multimers - proteinflex - flexweb - morph2stru - MotivatedMotifs - PDB News - VirusProteinStru - VirusProtStru -
- prot & DNA stru - ProteinQuaternaryStructure - membraneProtStru - StruAntibodyDB - StruFunctionDB - SFDBdoc -

 pdb format: bnl format - pdb format - pdb format - rcsb - ccdc -
PDB tools, fix H & res: tools - webPDB - DSvis - chimera - PDBTool structure validation - Domains anal (Altman) - webNormalMode - simulaid - pdbfixer -
 monomer 2 symmetry polymer: symmdock - Haddock - PDBePISA - Chimera - PQS - RosettaDock - ZDOCK -
Protein Surface Pocket: CASTp - Concavity - Concavity - protein cavities - PocketPicker - PocketPicker - DomainFinder - pocketmatch - pocketmatch - Fpocket -
Protein Comparison RMSD: ProFit - maxcluster - arms - GopenMol - Moilview - kabsch -


PDB-Ligand: PDBbind1700sbnih - PDBbind - bindingMOAD1400 sbnih - IridiumOpenEyeRefinedStru - SitesBase - SitesBase - scorpio - scPDBinding sites - scPDB - scPDB - RutgersLigandDepot - Relibase search prot-ligand (CCD) - Ligbase_ucsf - Credo - Credo - CredoDoc PDBsum - LunaPDBligands(Sayle) - biomedcentral - iRefindex - PDBligand - Molecules R US - Klotho(small compounds pdb) - TherapTarget - umich - Filippov - PepBank - BOND-BIND - BINDpsi - BINDpsi - BINDing(UMd) - PeptiSite - PeptiSitedoc - PLIC - PLICdoc -

bond order types from PDB in MOE Labute 2005 -

annotated comparative homology structure models: SCOPuniquefolds - Modbase_ucsf - swissmodel - 'protein classification' Search Pharm Rev - $EidogenTargetInfo - $AccelrysAtlas - Rosetta - Modeller -
Homology building: wiki - tutorial - SwissModel - ProteinModelPortal(PMP) - HHPredTuebingen - IntFoldReading - ModellerSali - Phyre - Robetta - Molsoft -
 Add loop: whatif - modeller - threading -

CYP P450 nomenclature - p450 - arabidopsis450 - SuperCYPinteraction - SuperCYPdoc -

Protein Location: OrganelleLocation -

Protein Function: prolink - prolinkdoc - wikiproteins - HPRD/HumProtRefDb - Uniprot - PRIDE - TCdbMembraneTransport - ProFunc (ebi) - genes2fans - ProtFAMilies - PFAMdoc -

DNA: Rutgers NDB: ndbsearch - ndbsearch - ndb - mirror at ebi - gopher
jena DNA drug stru - dna/protein -

sequence analysis page -

Biological DB: biomedcentral - NucleicAcidsRes - NAR112 - virus protein db

Biomolecular interactions

Systems Biology: GNSvisualcell - Caltech jpl models - Olivier - nrcam virtual cell biomodeling - virtualcellportal(sobj) - ecell - cytoscape mol interaction network - SysBioMarkLang - cellImageLibrary(bear sbe) -

Systems Biology Simulation Software: celldesigner - cellware - dynetica - ecell - gepasi - EMBLsmartcell - vcell - snoopy - CPNcoloredpetri - cellillustrator - mesord - MSspim - WeizmannBiospi - UNMcancersim - SalkMcell - AlbertaSimcell - UChiAgentcell - cell+ - ChemCell - MCell - Smoldyn - Smoldyn -

Optical Coherence Tomography: chen -
Allergenic Proteins: 800UTx -
Pheromones: pherobase -

big with big

yale links - ncib review - ConceptRel (tambis guest) - quaternary structures of multimers -

Protein interactions fall into three functional categories:
1) metabolic and signaling (genetic) pathways;
2) morphogenic pathways in which groups of proteins participate in the same cellular function during a developmental process; and
3) structural complexes and molecular machines in which numerous macromolecules are brought together.

Interactions pairwise between proteins:
DIP(ucla)
- 60k pairwise interactions between 20k proteins assessed visually by the thickness of the lines between two proteins and position of an interaction in a pathway.
BIND(ca) - interactions of protein-protein, protein-RNA, protein-DNA and protein-small molecule; presenting interactions from the molecular level to the pathway level.
Geneinfinity: workbench - tools -
MIPS(munich) - 2400 interactions with methods.
Proteome - protein interactions, function, localization.
Pronet(doubletwist) - protein interactions and signalling.
PIM(hybrigenics) - PIM - 1400 interactions of Helicobacter bacterium
Curagen - 1500 interactions of yeast proteins from two hybrid screen by S Field.
Prolexys - 280k yeast hybrid
PKU - protein protein analysis
HitPredict
DomminoDB


Noncovalent Bond Finder (Martz) -
MultiDock (protein-protein interactions) - pyDockTET -
Pronet (protein interactions db)
Pairwise Superposition
MOLMOL
Molecular Interactions, Protein-Protein : HPID/HumanProtIntDb - HPRD/HumProtRefDb - BIND/BiomolIntNetDb - DbDomainIntBind - DIP/DbInteractingProteins - Biogrid - corum - MINT - MINT - PPI - ProtProtInhibitors - string(embl) - STRING - STRING07 - brite - EBIprotprotInt - PIE - IntAct - IntAct - 2p2i - curaYeastPath - MyriadPronet - protein signaling AFCS - ZDOCK - SDOCK - NatalieQ - NatalieQdoc - EscherNG - Gramm - Haddock - Haddock - interdom - PDZ - pdbInteractions - PIN/ProtIntNucleus - POINTprediction - PSI - Domains anal of pdb (Altman) - proteomeCommons - GRIP - MLPK - PIAS - PIASdoc - Kohn(cyclin, p53) - flynets? - Manchester? - betasheets - PIM hybrigenics - hybrigenicsPIMRider Helicobacter - HelicobacterInteractome - XanthomonasInteractome - XanthomonasInteractome -
Genetic Nucleotide: RibosomeLinks - GeneNet - regulatoryGeNet - Transpath - Transpath - SVM -

Molecular Interactions, molecules: NCBI tools -

yeast two-hybrid prot-prot interactions: wiki - LittleUAz - campbell - aasland - biolprocedures - Collinge - bioteach -

protein DNA interactions: (Luscombe) - Rutgers NDB - PDI -
DNA-protein docking: EscherNG - DOT -

protein Lipid interactions (JBC) -

big with small

Biomolecular interactions, , especially Protein-Receptor-ligand/molecule (inhibitors & pharmacology): also see pharmacology page -

databases
#compounds (000 thousands)
#target activ(000 thousands)
ChEMBL - ChEMBLdoc - PHACTS - pharmatrek -
1000
9
ChemProt - ChemProtdoc -
1200
20
stitch (embl) 300 2600
Supertarget - Matador (embl) - doc
200
6
Bindingdb (Gilson) - BindingdbLinks
180
4
promiscuous (embl) - (doc)
25
10000
iPHACE (Oprea, es, channels)
800
200
carlsbad (Oprea) - doc - 430 1420
NIHLINCS - LINCS - LINCS - LINCS - LINCS - LINCS - 25 1+20
procognate (ebi)
25
7
DrugAdverseReactionTarget (sg)
1
1
TherapTargetDb TTD (sg)
17
2
DrugBank (Wishart) - T3dbToxinTarget -
7
4
DGIdruggene -    
PDTD
1
1
KeggPathLigandDB -    
SIDERadverse (embl)
1
4
PDSPKi (unc)
55
TDRtropics (sanger)
825
 
ChEBioInterest - ChEBIdoc -
30
PDBbind (Wang)
2
BOND (Thomson) BIND (Hogue) - lecture - doc -
11
     
TPDBsearch (UKansas) - TPDB - 1 1
IMIDIntegratedMolIntDb (FSU)    
PSMDB (toronto)    
TIPathogensTherap   5
Collaborative Drug Discovery (CDD) Lilly, Lipinski    


Binding Prediction for reposition and toxicity (also see Docking & ToxPredict): BindingdbPrediction - DRAR - Promiscuous(embl)Reposition - PromiscuousDoc - Promiscuity (scripps) - SePreSAdverse - TarFisDock - X-CScore (J Comp Aided Mol Des 16:11 2002) -
Binding Misc: ChartingChemSpace - prot catalytic sites (ebi) - SuMoBindingSites - TOPSligand - TOPSdoc - BourneLinks - SmallMolIntDbBlueprint - ChEA -

Protein Classification: PantherGO - info - info - info -

ENZYME (Protein-substrate): EC index by number: BRENDAenz&rxn - BRENDA - IUBMB - ECstatistics - BSM - expasy - QMW - nyu - PROW - EC pdb (ucl) - Japan - genomenet - AnEnPi - AnEnPi - ExplorEnz - ProBisBindingSites - ProBisDoc - EnzymeStruFunctionLinkage(SFLD) - SFLDdoc -
search: expasy - expasy - Worthington Enzyme Manual - Worthington Index - nih Selkov enzyme pathways - gdb search? - EC - kinaseclassif - KinaseGenome - plant peroxidase db - ECanal -

Metabolism: Enzyme-Gene-centric - WIT - Brenda - MetaCyc - patronov view - patronov constructor - patronov fig - visant - CarboxylEsterases - metab Predict in Comp Chem - oasis -

Chemical interaction & pathway db links: ChembioWishart - PharmbioAltman - BIND - BBID - DIP/DOE - links - CellBioModels -
Saccharomyces yeast cellzome - yeast pathcalling curagen -

Pathways data (most lack disease, drug, organ associations): biouml - ipaddiseasedrug - pathwayCommons - pathguide - animaps - biopathways consortium - pathwayAPI - pathAPI - NCInaturePID - SMPDBwishart - pharmgkb - pharmgkb - NIH - wikipathways - path2models - path2modelsdoc - navicell - navicelldoc - supertarget(embl) - UCSDnature - BioPAX - pathguidelinks - Reactome(EBI-GO) - quiagen - CGAP - CGAP - NCDIRinteractome - Biosilico - Biocarta - BioMeta - flipper - expasy BM - RocheExpasy - RocheExpasy - RocheExpasy - Recon - EdinburghHMN(BearSj) - spike - spikedoc - MPalign - Ariadne - AriadneMethod - Pathstudioprotdisease(AriadneGenomic) - daylightEmpath - panther - panther - netpath - AAASscience - STKE (Signal Transduction Knowledge Environ of AAAS) - GenMAPP - bionome - bbid NIA search - UMn - UMnMetabolicPaths - UMnDegradationPaths - soybase - yeast paths - sigpath - genenotes (entrez, omim, snp, kegg, swissprot, PubMed) - SPAD - also see protein interactions above - genego - PathArt(JubilantBiosys) - $GNS - $biobaseTranspath - ToxWiz&Pathvision(CambridgeCellNet) - VaTechMendesBiochNet - GasteigerBiopath - CSNDB - MRAD - phylosopher - puma2 - EMP - ovarian - INOH - hippronDynSignalingMaps - HDNhumanDiseaseNet - HuDiNeDoc - KOMICS - KOMICSdoc -
 KEGG vs Metacyc: Karp2013 -
 KEGG: KEGGmetab&reg(7k rxn) - kegg - KEGGapi - keggPromiscuous - kegg paper - KeggFiles - KeggFlux - KeggFluxdoc - UBViz3DKegg (sby 9On6MbxX) - OxyKeggNetwork - Prodorickegg - keggConverter - keggConverter - keggTranslator - keggTranslator - keggTranslator - BioMetakegg -
 Biocyc Stanford Karp: BiocycMetabpaths (Peter Karp Lecture - Karp - KarpSchema - metacycinfo - metacycinfo - metacycCaspi - SRIpathtools - pubs - ): BiocycSearch - BiocycBrowse - MetacycBrowse - MetacycSearch - humancyc - humancyc - aracycArabidopsis - EcoliCyc - PathTaxonomy - EcocycTaxonomy - BioDash - BiGG Palsson UCSD human - UCSD - LeishCyc - PlantCyc -
Pathways, parts: ROS/reactiveOxSpecies - Hahn & Weinberg cancer pathways - EnzMetPath - PI3Kinase In Cancer - ImmuneComplement - ImmuneComplement - yeast cygd mips - $symyx reaction path - simmune modl builder - FiehnMetabolites - UniHI - EcoliDisplay -
Pathways, Natural Product Pharmacognosy: McDonaldEnzymeDiagrams - purdue - pathDB (plants) - pathdb - AriadneResNetPlant - plant metabolites (Hamburg) - DewickIndex - phenylpropanoides - iridoid & anthocyanin (Stueber) - flavones - anthocyanin biosynth - iridoid - natural product synth - terpene cyclases Koenig - pathways$ - rapamycinsynth -
Pathways, regulation & signaling: 3DID - kyushu - BiobasePathoDB(sob) - TranspathSignal - Transpath - transpath transcription factors - TranspathXplain - TranspathDoc - TranspathDoc - Biouml - STC - arachidonic acid activation - Kohn(cyclin, p53) - $cience signal transduction - signaling-gateway (sobear) - afcs alliance cell signaling - afcs signal protein db (sobearj) - apop & p53 path - mitochondriaBeard - pathnet - pathnet -
GPCR: gpcr - cue - norakbio - druginhib - expasy groups - ShigetaMarkov groups - Athens - Qian - Graul - Graul - Karplus -
Pathways software: KeggChemBioruby - openbioJp - Bioruby - Alive - KarpSRIpathtools - KarpBiowarehouse - networkPortal - ariadnePathway - ubviz - iconixpharm - BioPathwayExplorer - bioDashHaystack - review - - metaall - metaall - PathCase - Biospice - ComPath - ComPath - spike - spike - keggConverter -
PathAnalysis: ComparisonConflict5db - CompConflictDoc - cytoscape - IngenuityPathKB - ingenuityPathways - GeneGo - GeneGoMetacore - 3omics - 3omicsDoc - BiowisdomSRS - NetSysBiol - NetSysBiolDoc - AriadnePathwayExpert - NCGR - informaxPathblazer - GenstructLogic - paracelPathworks - amaze - biochem path anal (Küffner) - Kuffnerpaper - Mendespaper - Pathblast prot prot int - MPASallignment - biopax path format - Moorthy paper - pathminerMcShan - interactome - explorer - genmapp - OspreyGenReposInteractDatasets(a98b59ah) - AnEnPi - $impheny - insilico - metaflux - MFAML - simpheny - pathfinder - PATIKA - pathcaseDB - MetaPathways - MetaPathwaysDoc -
Path Notation: SysBioGraphicNot - SBGN - SBGN - kegg2sbgn -
SysBio MarkupLanguage SBML: org - SysbioViewer - BEL - BioPAX - BELvBioPAX - BCML -

Brit J Pharm Guide to Receptors and Channels

Receptors: IUPHAR - IUPHAR - neuroreceptors - Nature2005 - NuclearReceptorDB - NuclearReceptorbase - guide - dblinks - ligands -

Channels: Yalechannels - ChannelPumpStru CMU - IUPSchannels - Nature2005 -

Pathways, metabolic: biocarta - Citric Cycle - MeteorMetabPredict - ADME Assoc Proteins - ADMETFeb04 - glycolysis -

Small Molecule Activity: ACL - Stockwell - holisticopia list -
Predict Biological Activity from Chemical Structure: PASS(sbe) - aboutQSAR - SOMFA download - PepBank -
Pharmacology page
Combo Combinations (see pharmtox): cytoscapeNetAnal - drugPredict -

Broad Gene-Protein info:

Biochemistry Principles: MIT - about - aminoacids - terpenes - Lectins Cermav - nobel - medbiochem -
amino acids: aminoacid properties - hydrophobicity AAindex - hydrophobicity ProtScale-ExPASY - MHPhydrophobic - HINT -

Human Gene DataBank: GeneCards(NIH) - GeneCards(Weizmann) - GeneCards(Weizmann) - ncbiguide - ncbimap - ncbimap - ucsc - Sanger - Sanger/EBI - GDB - GDB intro - OMIM - OMIM2k - OMIM2klinks - OMIM - UCL - aust OMIM search - OMIM GDB tutorial - NatureHumGenGuide - tigr hgi - So Afr EST - Tumor Gene db - HGP chromosome 13 - ornl Hum Gen Proj - gestec UT chrom 11 - NHGRI - NeuroNames (overruled by Carpenter's) - incyteProteome(sbearj) - ESTannotationMachine - NCIoncogenetics -

Gene Maps: biocarta - rat chromosomes (curagen) - brain gene map - Roche mouseSNP hapmap -

SOURCE search on UniGene dbEST SWISS-PROT GeneCards LocusLink
UniGene - dbEST - SWISS-PROT - GeneMap99 - RHdb - GeneCards - LocusLink -

Geneweb Cancer Gene links -

Apoptosis: Cell Death Society - Apoptosis on-line - NIH Apoptosis Interest Group - SciWeb Apoptosis reference center - Apoptosis Research Group (Canada) - Protomap - SoaringBear dissertation - Eerola dissertation - BAD genes - BAX (geneweb) - bcl2 family (Robens) - Nature -

angiogenesis: vlib -

bionet - biomednet (bear) - biomednet (sbearj) - carotenoids - biotransformation -

LINKS: biochemweb - Thys - chemdex supplies - sheffield chemdex - berlin - rpi - Pedro's - pomona - idt biotech - bulseco - biotech - CCL - NIU - UCD - UCLA - USDA Biotech - usda biotech - temple - chemfinder(sobear) - Oxford - Oxford - IU - Indiana 1 - Indiana 11 - Carnegie Mellon U - Whitehead mit - stanford - Harvard bio - Harvard gene - Rice - Cern (=w3) - CSU - CSU - Biol Data Transport - rockefellerU - usgs lib - einet galaxy - BRASS-Bioinfo Resource - Toledo Biol - Bio search - webWonder Science - harvard search - NSF fields of science - WWWworm:search 'chem' CCB (collab click bio-HIV, Citric Cycle) - Biomedical links (Monash) - Linus Pauling notebooks - BiotechMonitor - bio open repository -
Cytokines: NCIcytokines - Ibelgauftscytokines - acad -

Hormones: IndSt -

glycosyl-transferases Metabolic Pathways chem/physics gophers ibi biotech - tech transfer -

Natl Ag Lib:Biotech

Cell Biology Dict - BiolcourseUSC - cell bio UToronto -

Carbohydrates: Glycome Bertozzi - GlycosidicLinkages - CarbBank - UGaCCRC spectra - glyco - glycosci - glycosci - pangea gangliosyb - sweet builder - sweet builder - CellAdhesion - Carbodraw - CarbohydrateActiveEnzymes - medifast -
Glycomics: NIGMSconsortium - glycosuite - UNH - oxford - glycobiolText -

Lipids: Fatty acids tutorial (Baggott) - lipidlibrary - fatty acids (lipomics) - lipidmaps - lipidClassif - Chevreul - protein Lipid interactions (JBC) - fattyacidNomenclature - fattyacidChart -

Gprotein db

biospace

wisc Biotech

GFP & aequorin: biochemJ -

llnl biotech -

ORGANIZATIONS: SocExptlBio - PSEBM abst

csiro

 

Reaction & Kinetics

ibmCKS - CAMEO - Kinetecus - Kinetecus - EQS4WIN equilibrium - polyrate - Rxn-drill - MCA metab; kinetics IUPAC gas kinetics data.pdf - namedReactions - NMR stru/kinetics BMRB -

Microscopy: FSUprimer - nikon - iPALM -

Membrane Lipids (Beamer) - Glycerolipid (Beamer) - Lipid Metab (Isom, U Cent Ark) - Heerklotz lipid raft biophysics - MembranePDB -

Virology

NIGMS consortia: glycomics - lectins - cell migration - pharmacogenomics - pgen membrane transporters

Gene Disease relationships
medgene(sbj) -

GeneChips and DNA Microarray

animation - Brown(Stanford) - Nature1999 - OncomineArrayAnal - expression arrays -
Array annotation & visualization Guffanti review
DRAGONview
AffymetrixNetAfx - TIGR RESOURCERERcomparison -

Medgene LaBaer CoOccur 4k MeSH diseases X 53k NCBI genes (bearj) -Biogene - HarvardInstProt - LeBaerNature - LeBaerACS -

Genetics:
Epigenetics: NatureSpecialIssue -

BackCross Breeding: acf -

BioOntology: stevens - google - NISTbioblock -

Immune Epitope prediction: ctl - tepitope -

homebrew biotech: economist - dnahack - BiotechHobbyist - Agribiotics -

microbeworld

lab protocols: protocol -


© 1995-2014 Soaring Bear; your comments & corrections are welcome