Biochemistry (Soaring Bear)

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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