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

Biological function arises from detailed molecular structure and atomic interactions, making it difficult to overemphasize the role of structural visualization and biomolecular graphics in shaping our current understanding of the molecular nature of biological systems. [Mura PLOS Comp Biol 2010].

Molecular Viewers:
Rasmol: OpenRasmol - Sears quickguide - Martz raswin.hlp - umass - umass - ProteinExplorer - ProteinExplorer - berkeley - berkeley2.6 - rasmol(uk) - rasmol(Bernstein) - Molsee(rasmol aid) - Chime animation of Rasmol Chimesupport - rasmenu -
Chemical Spreadsheets: MarvinView: ChemAxon (MDL mol, Compressed mol, unique SMILES, SMARTS, Sybyl mol, PDB, CML, XYZ, POV-Ray) (bear j) - seurat - bioclipse - diva - accord - thirddim - spotfire - icm(molsoft) - quattro - isis -
Other viewers: Cn3D - swissDeepView - swissDeepView - AccelrysDSVisualizer - DSVisualizer - vmd(openGL) - zoomseq for VMD - vmdprot - iView - iViewdoc - axiom - moviemol(OGL) - Whatif (embl) - Moil trajectory - Moil(sgi suny)Visualize - rosettavote -  Molekel(lots of surface properties) - view & animate (Gaussian, Gamess, XYZ and PDB) - MolVis - PyMol - Chimera - qutemol - VidaOpenEye - Chem3D - Chem3Dwin download - Mercury CSD (pdb & mol2) - chime (sob rYRj7b; soab KNM3eX) - xmol (no further devpt) - viewmol (C download) - viewmol (C download) - viewmol (C download) - viewmol (C) - webspace - Molecule - VEGA - PNLecce - molden - molden - molden - molmol (unix,win) - MolWin download - tessel - povray(Win) - mol2pov - mol2pov - molsoft webviewer - molsoft icmlite download (win,sgi,linux) - molsoftbrowser - molegro - Molecules-3D - chemcraft - ORTEP (win) - Interchem (sgi) - Mehmacc -WebMol Java - UIUC Java - biodil linux - raster - raster - Pov - CACAO - Accord - AccelyrsDiscovery - Discovblog - AccelyrsDiscovery - accelyrsVisualizer - accelyrsVis - xbs(unix) - QMol - BioAdviser - NLMlist - Astex - SimbiosCheVi - BioSolveIT FlexV - verachem - sirius - bodil - theseus -
Protein Connelly Surface Cavity fill to view pocket cavities: MOE - CAST - Castp - SR - findsite - surfnet - molsurfer(embl) - MolSurf (molec surfaces, sketcher, smiles gen) - Laskowski Surfnet - pocketmatchPDF - prosurfer - tools -
Protein Superposition: Bodil - ProFit - LSQMAN - QMol - TOPOFIT - ARMS - CSR -
Kinemage: kinemage (download) - kinemage (download) - mage (download) - mage setup - kinemages kinemages? -
Trajectory: gOpenMol MD trajectory (Win,Linux,IRIX) - gOpenMol ccl - gOpenMol - XvidcapLinux video screen capture - CamstudioWin -
ChemMarkupLang (CML): xmlcml - Rust - wiki - tcaw -

Hbond display: MOLDEN - AutodockTools - Molekel(lots of surface properties) - SwissPdbViewer - HBplus -
SDeditor

STRUCTURE ANALYSIS:
RNA: RNADraw stru predict - RNA secondary stru - Mcsym predict - Ribosome db-uiuc - RNA folding -
RNA build: NAB - McSym -
RNA dynamics: NAMD - AMBER - LAMMPS -
Courses: VSNStmc - VSNSbiel - VSNSunige - VSNSmail - KahnUCSB - LevittStanford - GregoretUCSCBirkbeckPPS - Thakkar - Polik -
Protein Secondary Structure: NCBI Entrez - procheck - procheck (pps) - DSSP - ProSA, profit, etc (CAME) - Verify3D - Protein-spreadsheet - Prolysis:proteases -
Other Protein Structure Analysis: CATH - Cornell tools - Sternberg - LPFC - Gosper-ReView - uci software - G receptors - Ligplot-prot ligand diagraming - Ligplot - Ligplot - UCSF - Singh & Thornton side chain interactions - Thornton UCL - Hole (ion channels) - Simloc RMS - prot stru links - Vega - RAMPprotmodl -
Molscript ps presenter Baylor MBCR - tsai -
Water: GRID(Peter Goodford) - GRID - Dowser - Webmol(EMBL) - Solvent(Grubmuller) - CCP4 -

Protein Folding Prediction: scicentral - unibo NN - RPIrosetta - phyre -
Profiles-3D for protein model verification (Eisenberg): ucla - ucla - msi -

Structure Determination: XRAY XTAL crystalography: fourier explaination - xrayview - xray server - crystal lib - crystal - xtal packing - symmetry - search - tutorial - inorganics - inorg - shellx - arizona - karlsruhe - plane symmetry - pointgroups - aizman - spacegrouptbl - 230spacegroups - crowdphase -
BioMolec Cryst DB -
software: ccp4 - Brunger - O (SGI) - gsas - Xpow - CCP14 - Lazy Pulverix (fortran) - Oscail - Powder Cell (dos) - Rietveld - ricon - espoir (diffractometry) - espoir - Platon -
cutting a slab parallel to crystal plane: crystal - interprobe -
pKa of protein residues: Polaris(Warshel) -  


MOLECULAR MODELING

Tutorial: Young intro - Young intro - Turintro - Basic Modeling concepts - Milikan ex-acetylcholine - Hammes-Schiffer Modeling course notes - Gao - Cramer - Jensen - about - cache - cheminfoSousa - Jensen - wiki - CHARMonline - molcalc - molcalc -
Database of Simulated Molecular Motions - CompChemHighlights -
Links: claessen - Claessen - OSC - laaksonen - UTex NMR (Luxon) - nci-LMMB Bio-math - bio-online - arach - arach - caut - masakatsu - Concord Modeler - Morris -

Molecular Simulation concepts: Frenkel - Furio -
Problems with forcefields: Bear -
Forcefields: sprous overview - cvff - cheat (carboh) - yasp - antas list - Beachy comparison on tetrapeptides - Becker course outline - williams - FFdevelopment -
Dielectric Constants: clipper -
Atom types: atoms table(chamot) - amber - cvff - tripos - radii -
Atom & bond order parameters: NIST - BondOrder - aomix - MOE/CCG - bond order types from PDB in MOE Labute 2005 - ADF2005 - BOVIR -
DNA build: Bforshort - Namot for long -


COMPUTATIONAL CHEMISTRY Software: classen - boyle - biostorm sales - SIBIQ semi empirical orbital - CCL Links - asdn - sal list - yasara - AMICA(Gdanitz) configuration interaction - cambridgesoftChembionews(sobearj) - CS - CDK - CDK - MMTK - MMTKwin - RDK - PerlMol - JOELib - alchem - redbrick - bio open repository - interprobe - MMTSB - Avogadro - Avogadro - Avogadro - ExorgaSTR - scigress -
Structural Biol Software: UIUC - UIUC -
rubyChemkit -

Chem Database: JChemBase - JChemBase - acdChemfolder - Chemaxon (bearj, sbej) - CambridgeChemfinder - Daylight - MOE - sMol Explorer - Tripos - MDL - Synopsys - Maybridge -

CompChem archive, jobs, journals, software, latex - CCL99 - CCL98 - CCL archive - compSciEng - antas list - latrobe list - stuff - combinatorial db - csir - Chem under Linux - Mol Bio under Linux - ChemInf list - ChemLinux -

Cheminformatics: IntlConfChemStru -
Reaction Modeling Transition State: Gallagher - orca -
Metabolite Catabolism: catabol - metasite - metasite - oasis -

QSAR

Information: Intro(Richon&Young) - history(VanDrie) - QSAR Soc - about - ACS/COMP links (SAR, jobs, acad, meetings) - history Parascandola - LeoLecture -

PASS online prediction - Dragononline - Osirisonline - insilicomolecule - Jin/UNC description & calculator - QikProp(Jorgensen) - capsaicin QSAR - PLS - QSAR & Modelling Society - BioByte Pomona - Pomona Medchem-QSAR - QSARpartitioncoefBiobyte - pomona smiles - daylight - open3Dqsar -   PLS fortran (Ponder) - NCI SAR DB - parameters - J Curr Pharm Design - Ertl&Jacob web tool - PharmTree(930-27-5108) - LassoSimbiosys - codessa - quasar - Quasar - lohninger - lohninger - knime - smog conformer gen - ConCOORDconformgen - smog - molscan - mol2mol, sterimol - Protherics Crunch - chemdesign, chemx - ChemDescrip - NN (win) - NN (win) - ECOSAR - ecosar - ecosar download - oncologic - MatlabPLS - HASL - HASL - VaBiotech - Scivision - MOE/CCG - XCScore - MIPSIM molecular interaction potentials - Pharmtree - X-CScore (J Comp Aided Mol Des 16:11-26 2002) - libraria - HESI QSAR - HESI QSAR db - DSSTOX EPA ToxQSAR - DSSTOX EPA ToxQSAR (ACD) - Qtox - JOELib - Octet - sourceforge - CDL - Moldiscovery Grid, Metasite - MOEpharmacophore - vlife - mcqsar - Spls - Pentacle - Dmax - open3Dqsar - 3Dqsar - cresset - DotmaticsVortex -
COMFA:
SOMFA: SOMFA - SOMFA2free -
Superimpose alignment: interprobe - CSR - MIPSim - swiss pdb viewer - Mol2Mol - VEGA - open3Dalign - shaep - phast -
Molecular Similarity: MOLPRINTsimilarity - similarity based on geometry - MEssEM - MIPSim - Guha - decoyfinder -
GeneticAlg: GA - GA - GA - Clark(cisrg)  - genetic -
Python: dalkebasics - beginner - tutorlist - biopython - daylightPython - python - python workshop -
SAR descriptors: Dragon - Edragon1600 - EDragon - MarvinBeans - ACD - TSAR - myStructure - Feher&Schmidt -

ADME prediction: PASS online prediction - VCCLabonline - admetus - petra erlangen - admetox - ADMETboxes - admeBoxes - QikProp schrodinger - Solubility acd - iDEA lion - C2 accelrys - PreADMET - NCI Lipinski5 search jchem - jchem Evaluator - PharmaAlgorithms - Qpharm - qADME - volsurf - GilsonBindingPrediction - ontomine -
Metabolite prediction: Topkat - Case - derek - treetox - hazardexpert - pallas - metaprint - Metabolizer - metabolynx - acd - someviz - p450someviz - p450metapred - p450Smartcyp - p450Reccr - bioclipse -

Activity Prediction: SuperPred - SuperPredDoc -
Target Prediction: ShoichetSEA - SEAdoc - IMMD - IMMDdoc -
Toxicity Prediction: insilicofirst - derek - derek - Casetox (Klopman) - CASETOX - Topkat (accelrys) - EPAecotox - epaIRIS - ITER - toxboxes - toxtree - toxtree - DSSTOX EPA ToxQSAR - DSSTOX EPA ToxQSAR (ACD) - Qtox - FAF - TPS-SVM - ToxPage - OECD -

HTS: ClassPharmer - leadid - SONNIA (KMAP) - MOE QUASAR - SARNavigatorTripos - PharmaAlgorithms - Chemaxon - Accelrys -
Data Handling db: FDA informatics-
SARchemdb: JOElib - JChemBase - chemnavigator - IDBSchem - PowerMV - MolTable - BenderDatasets - lion/biowisdom leadnavigator -
Functional Groups: checkmol -
Conformation: balloon - molgen - frog - msdock -
Drug mRNA Connectivity: broadCmap - thomas - Lamb06 - Lamb2 - Lehar07 - Li09 -
Protein-protein Interaction Drugability: pias - piasDoc -

Chem Properties

Chem Calculators: MartindaleUCI -
Ti
Solubility & logP prediction: VCCLabonline - VCC - VCCalogps - logP explained Leitl - Tetko - YC Martin comparison - Aquasol (Yalkowsky) - Freesolv - MarvinPlugin - EPASuit - daylight - pomona - InteractiveAnal - virtuallab - sparc - acd - chemaxon - Kow (syr) - kow - predict solubility from smiles (syr) - LOGKOW - Autologp - AlogPs - chemsili - logP clip - logP CHEMICALC_2 608 (qcpe) - Grunenberg - compudrug - qpharm - PlogPftp - PlogP docs - moka - scivisiontest - scivision(win) - xlogp(unix) - xlogp - mol draw and calculate logP, surface area, Rule of 5, etc - Hint - platinum - molcalc - molcalc -
Stouten solvent refs - Vega -
Solvation: solvate - ChemSol(Warshel) - Solvation & Dispersion(deVries) - solubility modeling (Stouten) - cosmotherm -
Warshel(USC): Polaris, Enzymix, Chemsol -
Properties: EPA-EPISuite - Sparc - Sparc - QMPR - leadscope10k drug properties - Cosmo solubility - silicos -
pKa: Marvinonline - Marvinplugin - SparcUGa - opium - leito -
Boiling Point, vapor pressure: MPBPVP -
Thermodynamic equilibrium of 2000 simple compounds: NASA - NASAdocs -
comput fluid dynamics
Volume: ASV - csb - Chimera -

Chemometrics:

terms - Alchemist - links - Trygg - wiley - eigenvector - NAmICS - Russian - muni - chemint -

Conformers

HyperSpin - HyperSpin - BOSS/MCPRO Monte Carlo (Jorgensen) - Monte Carlo -
Monte Carlo: QMCMOL - QMCBEAVER - CHAMP - ZORI - CASINO -

Conformer Generation: smog - ConCOORD - Verachem - balloon - divcf - dg-ammos - omega - confab - acs - frog - rdkit - corina - MOE - chemaxon -
Tautomer Generation: OpenEyeQuacpac - MolNetTautomer -

Docking

Villar review - Olson Autodock - Autodock - AutodockTutorial - AutodockTutorial - AutodockHowto - AutodockList - Autodockserver - AutodockMezeitool - AutodockAntibiotic - dockingServer - mgl - AutodockVina - DockoMatic - DockoMaticDoc - istaridock - istarDoc - AutoCRL - docktools - kuntzDock - ucsfDock - ArgusDock - FRED(eyesopen) - MolegroMoldock - Moldockdoc - Molegro (JMedChem) - molegro - molegro12prot386plantchem - simbios - simbiosEhits - EhitsBest - Ehits - hotdock - Protherics Crunch - xsite - ICM - ICM (Molsoft) - molsoft ICMlite download (win,sgi,linux) - Vakser - Vakser molec matching - DockVision - Situs(J Stru Biol 125:185 1999) - 3ddock - FTDock (Sternberg) - MultiDock (protein-protein) - Escher - BMMdockLinks - Grasp - FADE-PADRE - FADE-PADRE - PASS - GOLD - biosolveit Flexx (Lengauer) - Flexx - Glide - SPROUT - SPROUT - newlead - newlead - leadfinding - BDTautodockautomator - Cidrux - GDB - GDB - GDB - 3DFS - quantum - haddock - zdock - escher - rosetta - plants - fitted - gemdock - argus - rosetta - accelrys - vlslinks - ProtLigANT - sitemap - fpocket - PythDock - mcule - pierr - TarFisDock -

Virtual Screening (vs): software - AutodockScreen - Molinspiration - DovisScreen - pocketmatch - pocketmatch - FieldScreen - Flap - PhAST - CressetFieldstere - Dockres - Dockres - VSdocker - vinaworldgrid - visiscreen - GilsonBindingPrediction - SEAshoichet - pharmMapper - vina - Ontomine - LeadFinder - LeadFinder - discus -
  Chemical Compound Screening Libraries for diversity: wiki - Biospecs - 200k chemstar compounds for screening; SDf (chembase, isis, maccs) format - asinex - ChemNavigator(sobear11j) - inteligandfragments - ScreenLibPharmTox - dekoisDecoys -
  Scaffold Hopping: ShaEP - Flexophore - LigCSR - LigCSR - 1click - ScafBank - Lasso - LassoChemSpider - ROCS - SHOP - Recore - SuMoLig - CODESSA - Topomer - Cresset - FieldScreen - topomers - TargetFishing -
    presentations: Wagenerppt - Waleppt - Tsunoyama08 -
Solvent Accessible Surface Area (SASA, Connolly surface): surfnet - submit mol2 to ASV - Protein Active Site Spheres (PASS) - Qsitefinder - MSRoll - MSMS(olson) - MSMS - GPOL93 - VEGA - NACCESS - SIMS - icm - Taverner's steric - Grasp - VOIDOO - VOIDOO - antas links - area (ut) - ASC - embl - eisenhab embl - asc-embl - nsc-embl - nsc for Hinsen - stanford - ACCESS yale - Naccess fortran - Naccess - Deepview - ICMlite molsoft - VMD - marchingcubes - MOLSV QCPE QCMP053 - hobbes steric - whatif - dodssp - MolMol - Sybyl- SwissPDB - gOpenMol - Molekel(lots of surface properties) - ESCHER DNA-protein docking - DMS -
Shape based: USR - USRballester - ESshape3D - ROCS - ShapeSignatures -
Entropy Enthalpy Compensation: Huber - Jogalekar - Sharp - Adams - Adams - Qian - Steffen -
RMSD: QCP -
Bear's modeling DNA Interacting Compounds for Cancer Therapy -

Binding Interactions - go to biochem page

Drug Design

Success Stories: Ulcers -

NCSC comp chem ed - NCI - NCI SAR DB - Palma - Kahn - Swain - Display types - chem Animation - Keck (Rice) - EMSL/MSRC Home - UGeneva - Monte Carlo - CADD intro-Balbes - drug design-Oshiro & Kuntz - LigBuild - sprout molec design - Cidrux - ncadd (java) - Oshpiz - Pharmscape - beilsteinSymp -

Drug Design Software: rasse - autogrow - LigandBuilder - Ligbuilder - Sprout - sprout molec design - Autobuild - Ligandscout - wvu -


Alignment: FBSS - PowerFit, SEAL - FlexS - pharao - piramid - piramid -

Modeling Theory

NIH Molec Modeling -
Molecular modeling in Education: NetScience - MacKerell - Cousins - Boyd - ICC - PCdemos - martindale - SimChemistry - ccp2 continuum - Steinbach - Savary - ContinuumElectrostatics(Gilson) - cache links - ucsbKahn - SousaLisbon -

Molecular Diversity

diversity forum - 7/97 conf -
Gronigen: Condensed Phase-deVries - Solvation & Dispersion-deVries -

Quantum/ab Initio

Tutorials: CCM - qcii - ICC - Cramer - orbimol - young - chemie - msi - wilson(ucsd) - colvin(llnl) - protein - TS - TS - accvip - symmetry - symmetryGoss - BSSE - Marx & Hutter theory 150 pp 2000 - QM MIT course - QMcontinuum - QuantumSimulations - NBO -

Gaussian: G94 keywords - gaussian beginners (Young) - Hammes-Schiffer course notes - wilson - course sylabus - course outline - DFT Molfdir MOLSCATtering - gaussian - gaussian conv - Columbus - Bader - function gradients - QClit (7209) - DeFT - DeFT - QuantNT - crdb 211 mol - Turbmole - ChemcraftSymmetry - Symol - Fract>OrthonormalConvertAngel -
Gaussian98W's IOp list: gaussian - gaussian - gaussianarchive - jussieu - jussieu -
Gamess: Gamess (ames) - Gamess unix - Gamess PC - PC GAMESS (ames) - PC GAMESS (msu) - webinterface(msu) - PC Gamess - Gamess (ac) - Gamess (ac) - listserv archive - Gambuild interface - GamessScripts - GamessScripts - GhemicalGAMESSGUI - gamessTutorial - gamessTutorial -
Gamess Orbital Plot with: Chemcraft - MOLEKEL - PC GAMESS - AOMix - Gamess: PLTORB keyword in the $CONTRL section of Gamess' manual, then as stated in the gOpenMol pages, use Gamess2plt to convert a Gamess "cube" PUNCH file to a plt file. For Mac, MacMolPlt is the easiest.
Other: ICON-EDiT download - dalton - Huckel - Huckel - HuckelCalc - PSI3 - Crystal Hartree Fock - q-chem - q-chem - Cray Unichem Mndo, DGaus, Cadpac - Delphi, Grasp electro surface - Shrodinger initio - MEP - Tamulis - ADF - JEEP Car-Parrinello initio/dynamics download - fhi96md - Fritz-Haber Car-Parrinello (fortran download) - xvibs - xvibs animation - excited states - AIMPAC el density download - AIMall - BatchMan interface to Mopac, Gamess and Babel - NWChem - NWchem - NWchemviewer - WebMO interface (for Gaussian, Mopac & Gamess req. unix server) - Symmetry point groups - Dirac - AOMix orbital interaction - Orca - Orca - MoCalc Interface for Gamess, Mopac, Tinker - vasp - vaspblog - zodiac - asdn - Chemissian -
Orbital Density Display Viewers: SURFER - AVS - VU - Gnuplot - gOpenMol - jmol - jmol - molekel - molekel - Molden - Molden download (unix/vms) - Molden download - CACAO - ReView - MOLEKEL view & animate (Gaussian, Gamess, XYZ and PDB) - MolWin - MolWin - MolWin - Rasmol - NonCovalentInt - pgplot - vibration animation - MOMIX - Joubert download - Molnff - viewmol download - viewmol download - xvibs - xvibs games modules - Vibration modes Win - Ramazanov - openDX - xmakemol - Zaldini 4Dview - obbligato - Voxel - Voxel - COSMO - Zoa - SWizard - AOMix - ChemCraft - theochem - Facio - Gabedit - WebMO - SchrodingerMaestro - Facio -
Gabedit GUI Gabedit for Gamess, Gaussian, Molcas, Molpro, MPQC

cartesian<>zmatrix: ccp1gui - Mol2Mol -

Ab initio Basis sets: basis set intro - EMSL(PNL) - EMSL(UK) - EMSL (UK) - stuttgart - molpro - Transit Metal 631 - DGauss - DGauss (cmbi) - DGaus (cray)? - DFT (cmbi) - wavefun - antas links - chamot - karlsruhe - sauer - juanp -

DFT: DoD - FHIMD - MPQC - deMon2k - orca - demon key dft metals - demonkey - muenster - turbomol - firefly -

Semi-Empirical
Mopac: manual - M2kmanual - manual(Schrod) - thys links - Stewart? - M2k - Errors - Errors -
Mopac download: ghemical - Ghemical (mopac, HF, MM, viewer) - Ghemical - ufl - ufl 6-Win95 - 6Win(ccl) - 6Win(ccl) - ccl - 7(ccl) - 7(ca) - osc - osc - osc - osc - osc - chem2pac - oakland - oakland - MolEdit Mopac editor - mopac converter - 6softshell - @puchta - chemconsole - VEGA/mopac - mopac editor - winmopac -
other semiempiracal: semichem AMPAC - MOZYME (Stewart) - Argus download - Argus - zindo (UFla) - educhem - multimode - Sparkle for TransMetals - ColumbusGNU - Molcas - deMon2002 - Dynamo -
ONIOM: morokuma - humbel -
crystal challenge

QM/MM: roar - NWChem - gamess/charmm -

Enthalpies (18 methods, 9 basis sets) for 600 small (>6 heavy atoms) NIST CCCBDB

Valence Shell Electron Pair Repulsion (VSEPR)

Explicit installation instructions for RedHat Linux along with GAMESS, MOPAC7, Gaussian98 & PortlandF77

Molecular Dynamics and Minimization:

OnlineCompChem: CSE(bj) -
Charges: Gasteiger - OPEP charge fitting - RED for ESP charges - Vcharge - ddec -

Molecule Building: xiangjun 3dna - Beveridge - aten - avogadro -

Allen & Tildesey's "Computer Simulations in Liquids": CCP5 lipids - CCP5 lipids - CCP5 lipids - CCP5 lipids - CCP5 lipids -
Membrane: Heller - Heller - umass - Robinson's membrane builder - membuilder -
Gas: Collide (win) -

Software: LAMMPSsandia - softshell - CSEO - tantalum links - CPMD - fantom - antas links - torleif - Rapaport - RAMVIB (fortran) ff refinement - DL_POLY (fortran) - NAMD (parallel OO MD) - EGO (parallel MD) - EGO (parallel MD) - AMMP (win,unix) Harrison - pimm-scf (fortran) - Q(Aqvist MD of solvated molecules) - kachina - Uppsala Mol modl tools - globalmin - chemaxon - gabedit - cp2k - zem - zephyr - DEShawDesmond -
GUImodeling: Ghemical - Ghemical - zmatrix - Facio - ChemCraft -
Software Catalogs: chemsw - camsoft - softshell -
Download: ProtDynamServerNIH - FANTOM (unix) - PyMOL - PyMol - PyMOL - molsoft icmlite download (win,sgi,linux) - moldy - GROMACS - GROMACS - GROMACS - DL_POLY - chem2pac - Concord Modeler - biomer -

thermal ellipsoid: ortep - ortep win - Oscail -

Annealing: Frost - Carter -

Software Documentation

MSI/Biosym: home - docs (msi/msi-doc) - support - old home - basie docs - cvff - topics - dcl Apex - WebLabView - quanta tutorial - Dibug archive -

AMBER changed from amber.ucsf to amber.scripps: scrippsAmber - scrippsDocs - ucsf Amber - new params - ions - Kunz - D Case - oxford amber - cliff interface - parm interpolation of C,N - roar - amber convert - AmberParmDB(Bryce) - docs - AMBER > NAMD - RESPchargecalc - RESPchargecalc - RESPcalc - RESPcalc - q4md - GPU5x -

NAMOT : docs - home

Tripos: Sybyl - Tripos - mol2format - DBFILTER check mol2 -

programs that add hydrogens: Amber - ArgusLab - Mol2Mol - kinemage - Weblab - WhatIf (also optimizes H network) - whatif - SwissPDBviewer - HyperChem - pdb2mol2 adding H & charges -

programs that calculate dihedrals: VEGA - Mol2Mol -

Other Modeling Software:
Molgen - Molgen - Molgen -
GROMACS - gromacsOpenMM - gromacs MD (linux) - Gromacstutorial -
Wavefunction Spartan - Spartan/Gamess/Gaussian -
MacroModel - MacroModel - MacroModel docs -
HyperChem - HyperChem demo -
CHARMM - Charmm doc - Charmm doc - charmm list - charmm param - charmm param - charmmparam - charmm traject - docs - docs - tutorial
scivision -
QCPE (osc) - QCPE ftp - QCPE email -
XMol(umn) - XMol(msc) - Xmolftp - XMol faq xmol(chemie) - xmol(dresden) - xmakemol - note: xmol incompatible with irix 6.2 (jtgolab@amoco.com).
Other Modeling: xbs - xmakemol - molekel - PyMol - vlife -
Cambridge Cadpac - Oxford Mol - Sculpt - biomednet/shopping/software to get sculpt - CCG - hinsen mmtk -
erlangen various - vr RealMol CAVE -
argus - ArgusLab 3DMolecule Builder, MM, QM -
Visualize
Modeller - protein & homology
Moloc free for academic: Moloc - MolocDocs - MolocDocs -

Free/open source 3D modeling: PyMol (Win, Linux) - Ghemical - openscience links - GDIS - gabedit -
3Dedit Mol2 handling: XdrawChem - Dynamol - MarvinSketch - PRODRG - CCP1GUI -
Build PDB files: Weblab - VEGA - VEGAZZ - Molekel - TINKER dyn,min (fortran) - ECEPP -

Unix: UNIX help - unix/York - C/unix C++ course cmu Perl - UF Perl - metronet Perl5 - LinuxSciAps - BioPerl -
Unix web vulnerabilities: 10pht - rootshell - cert - netcomp -

3Dmonitor

SGI SGI - graphics convert - freeware - g77 binaries -

Other docs: Fantom minimizer - IRIS Explorer -

Software downloads: Genamics - Molgen dos download (builder, mopac, MM2, logP) - Mopac - Huckel - CactvsAcad - CACTVS builder - cactus SDF toolkit - Accord viewer - ISIS/Draw (download) - Isis convert to 3D(acd) - gar2ped - re_view - simtel chem - SDSC: Shape, Flex, Xtalview - cacao plot (PC) - squid md (SGI) - MMTK tools - MMTK tools - osc ftp - osc gopher - molwt (win) - biomer - VisualizeMolecules-3DBioCoRe - MOLDYN neutron scattering MD - linux4chemistry 24 programs - linux4chemistry - tinker dynamics (fortran) -

Software descriptions: claessennetsci - netsci - qcpe - NIH list - synopsys - Antunez table - MicroSim - Solvate - osc - NIH or GROMOS-MD Gunsteren - GROMOS-MD Gunsteren - ncsa - bital imaging - gOpenMol MD trajectory - gOpenMol MD trajectory (Win,Linux,IRIX) - gOpenMol ccl - moledit - Jamberoo Jmoleditor - CCL - AM-Galaxy - scitech catalog - Deumens links - Interprobe - yasara - chem&mbio - Thakkar suggested software -

ChemKey demo

CAS/Mime definitions - chemmime -

Beowulf cluster: beowulf - arizona - kumar - IEEE - ClusterComputing - extremelinux -

Brunger's Xplor - Brunger's Xplor - XPLOR - xplor tips - ribbons - MetalSearch (replaces aa with Cys/His to make zinc finger); - Parallel Molec Dynamics - CCP minmd - hobbes conformer pucker - molec viewer - microsimulations -

Analysis:
Multipole moment: PDM (qcpe) -
MDXVU -
Kintecus - kintecus - kintecus -

hardware benchmarks: ki - pnl - pnl
PS3/Nvidia: ps3grid - acelleraCellMD - nvidia -

Chemical Structure Description formats: CTformat -
InChi: iupac - cambridge - wikipedia - acd - Heller - pub3d - Apodaca - ninja -

SMILES test structures:
Hexahelicene c1ccc2ccc3ccc4ccc5ccc6ccccc6c5c4c3c2c1
Nonahelicene c1ccc2ccc3ccc4ccc5ccc6ccc7ccc8ccc9ccccc9c8c7c6c5c4c3c2c1
Polyacetylene C=C-C#C-C#C-C=C
SMILES tutorials: pomona - pomona - open - daylight - theory(daylight) - daylight links - tutorial Leitl - smartstheory - schiele - NCI db smiles - aa - OEChem - dalke - dalke - Syr - CAS>SMILES Syr - specification -
SMARTS: daylight - daylight - cpanparser - perlmolparser - smartsview - smartsview -
SMILES conversion: OSRA - OSRA - synopsys - uniquetizer epa - ChemAxon - MolSurf (molec surfaces, sketcher, smiles gen) -
SMILES > 2D: cactus - cactus - CDK - bkckem - xdrawchem - openbabel - molnet - Apodaca - campdepict - OghamLexichem -
SMILES > 3D: Guha - Guha - Frog - openbabel - molnet - ChemaxonMarvinMolconvert - corinaMolNet -
SMILES viewer: mpice -
SMILES viewer online: colby3Dmin(chimeIE) - cactus>GIF - erlangen>GIF - erlangen>gif - corinaErlangen - DaylightDepict - $Straus>3D -
SMILES structures: Syr 103K pubchem -
SMILES open source: OpenBabel (C++) - JOELib (Java) -
SMILES from name converter: excelcdk - chemcell - opsin -

Format Conversions:
Babel: openbabelserver - openBabel - openBabelwiki - Babel(smog) - Babel(eyes) - Babel(softshell) - Babel(ccl) - Babel(ccl) - BabeltutorialopenBabel(sourceforge) - BabelWinCCL - BabelWindoc - Babel(ua)? - Babel(ua) - ncsu - easyWinBabel - Babel(Dolota?)PMRustCambridge - Pybel -
Other: Cactus smiles, sdf, pdb, mol - Cactus - MolecNetworks - 2dcoor - Cliff - Cliff - Iinterpret - mol2mol summary - mol2mol download - Mol2Mol - mol2format - Vega - ViewerLite - amber/iupac - chem2pac - Interchem (mol, mol2, car) - pdb2gif - hyperchem2mol2 - MolConverter in Marvin Beans (ChemAxon)(bj) - mol <> pdb convert & display - pdb2mol2 adding H & charges - AMBER > NAMD - cif>pdb(Mercury,CCDC) - Mercury CCD - platon - Platon cif files - Ortep - EnCIFer - bernstein - rutgers - MDL>SMART(MOLSMART) - MOLSMART - MOLSMART - PRODRG2 - prodrgonline - SparcSmiles>2D -
2D->3D Convert: Corina - Corina - Corina - Corina - Corina - Corina - Chemreader - asterix - asterix - molgeo - smi23d - smi23d - cubic - weblab - CLiDE SimBioSys - OSRA - osra - acd3D ISISIsis(acd) - Comspec3D - Cybermol - ACD3D - scan2D>3D - Kekule - chemOCR - marvinChemaxon - Balloon - DG-AMMOS -
3D->2D Convert: 5toolsApodaca - GifCreatorNCI(smiles/mol>gif) - Bioclipse - GifCreatorErl - GifCreatorErl - GifCreatorErl - CactvsErl - xemistry - interchem - CDK - chimera - draw2d - ChemaxonMolConverter - ChemaxonMolCon - CA - openbabel convert to SMILES and then Xdrawchem input and save - MolConverterMarvin - MarvinBeans - ChemDevelopKit - JChemPaint - OghamOpenEye - rajarshiSDF2JPG - MOE - jamberoo - mcinchem - mcinchem -
atom names: UCSF/MSI/XPLOR/SYBYL - Jmol g98 - chimeral - aimwin - molda - amber convert -

name structure: Lexichem Open Eye (Acad-free) -

VRML: Conversions: erlangen - darmstadt - pdb2vrml - pdb2vrml - pdb2vrml - xtal3d download - pdb2vrml download - lemans - MMTK - weblab - vmd - zeus - molda -
Examples: P450 ex - Robinson's membrane builder - chem vrml -
MDL format - MDLmolSpecification - MDL/SDF format - SdfFormatEPA - SDFtoolkit - UNIIcode - CTformat -
open software to parse MDL Molfiles: OpenBabel - CDK - JOELib - Rosetta -

Combinatorial Chemistry: netsci basics - loudon - chemplace $50/yr - warr - warr links - netsci - netsci7 - netsci3 - netsci2 - acs - bri - combinatorial db - afferent - CSPS supplies - Mol Diversity J - J CombiChem & HTS - diversity info - vesta combichemlab - combichemnews(bearsmail b) -

Spectra calculation: PWSCF IR&Raman - CASTEP - SWizard - SWizard - SWizard - webmo - GaussSum - GaussView - Origin -

Chemists & listserves: sci.chem, newsgroups - Chemists - Listservs - chem listservs - chem listservs - chem listservs -

Retro-Synthesis & reaction: chemkey - koen - unl - syntree - syngen - syngen - spurt - Jorgenson'sCameo - Cameo - holowin - lhasa - synchem - wodca - dendral - theresa - chemaxonReactor - simbiosys - scifinder -
Organometallic: ilpi - inorganicXtal -

ECCC-1 11/94 - ECTOC 6/95 - ECTOC discussion - EGC-glyco 9/95 - BioInorganic - BioInorganic suny - zurich - polymers - heterocycles beilstein - beilstein - zvon beilstein tutorial -
Units conversions: about - berlin - uio -

Chemogenomics: Iconix -

Supercomputing: NSF: PSC - SDSC - NCSA - OSC - CTC; DOE: NERSC - PNNL - Alabama - BarcelonaBSC - CESCA - France IDRIS and CINES -
gridchem

Traveling Salesman Ant Colony Pheromone optimization: Maniezzo - Gambardella - GambardellaPSU - Dorigo - ACOsoftware -

People: Parthiban Srinivasan -


?1995-2006 Soaring Bear; your comments & corrections are welcome