SOARING BEAR Ph.D. Pharmacology
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Scientific advisor to the health professions &
herbal industry
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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 -
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)
-
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 |
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ChEBioInterest - ChEBIdoc - | 30 |
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PDBbind (Wang) | 2 |
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BOND (Thomson) BIND (Hogue) - lecture - doc - | 11 |
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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®(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 -
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 -
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 -
GFP & aequorin: biochemJ -
ORGANIZATIONS: SocExptlBio - PSEBM abst
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 -
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 -
lab protocols: protocol -
© 1995-2014 Soaring Bear; your comments & corrections are welcome