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

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 - vmd(openGL) - zoomseq for VMD - 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 - 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 - Molecules-3D - chemcraft - ORTEP (win) - Interchem (sgi) - Mehmacc -WebMol Java - UIUC Java - biodil linux - raster - raster - Pov - CACAO - Accord - AccelyrsDiscovery - accelyrsVisualizer - xbs(unix) - QMol - BioAdviser - NLMlist - Astex - SimbiosCheVi - BioSolveIT FlexV - verachem - sirius -
Protein Connelly Surface Cavity fill to view cavities: MOE - CAST - Castp - SR - surfnet - molsurfer(embl) - MolSurf (molec surfaces, sketcher, smiles gen) - Laskowski Surfnet -
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 -
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 - 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 - 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 -
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 - Basic Modeling concepts - Milikan ex-acetylcholine - Hammes-Schiffer Modeling course notes - Gao - Cramer - Jensen - about - cache - cheminfoSousa -
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 -
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 - 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 -
Structural Biol Software: UIUC - UIUC -
rubyChemkit -

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 -

QSAR

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

PASS online prediction - Dragononline - Osirisonline - Jin/UNC description & calculator - QikProp(Jorgensen) - capsaicin QSAR - PLS - QSAR & Modelling Society - BioByte Pomona - Pomona Medchem-QSAR - QSARpartitioncoefBiobyte - pomona smiles - daylight 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 - 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 -
COMFA:
SOMFA: SOMFA - SOMFA2free -
Superimpose: interprobe - CSR - MIPSim - swiss pdb viewer - Mol2Mol - VEGA -
Molecular Similarity: MOLPRINTsimilarity - similarity based on geometry - MEssEM - MIPSim - Guha -
GeneticAlg: GA - GA - GA - Clark(cisrg)  - genetic -
Python: biopython - daylightPython - python - python workshop -
SAR descriptors: Dragon - Edragon1600 - EDragon - MarvinBeans - ACD - TSAR - myStructure - Feher&Schmidt -
ADME prediction: PASS online prediction - VCCLabonline - petra erlangen - admetox - ADMETboxes - admeBoxes - QikProp schrodinger - Solubility acd - iDEA lion - C2 accelrys - PreADMET - NCI Lipinski5 search jchem - jchem Evaluator - PharmaAlgorithms - Qpharm - qADME - volsurf -
Metabolite prediction: Topkat - Case - derek- hazardexpert - pallas - metabolynx - acd -
Tox prediction: insilicofirst - derek - derek - Casetox (Klopman) - CASETOX - Topkat (accelrys) - EPAecotox - epaIRIS - ITER - toxboxes - toxtree - toxtree - DSSTOX EPA ToxQSAR - DSSTOX EPA ToxQSAR (ACD) - Qtox -
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 -

Chem Properties

Chem Calculators: MartindaleUCI -
Ti
Solubility & logP prediction: VCCLabonline - VCC - VCCalogps - logP explained Leitl - Tetko - YC Martin comparison - Aquasol (Yalkowsky) - MarvinPlugin - EPASuit - daylight - pomona - InteractiveAnal - virtuallab - sparc - acd - 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 -
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 -
pKa: Marvinonline - Marvinplugin - SparcUGa -
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 conformer gen - ConCOORDconformgen - Verachem -

Docking

Villar review - Olson Autodock - Autodock - AutodockTutorial - AutodockHowto - AutodockList - vina - docktools - kuntzDock - ucsfDock - ArgusDock - FRED(eyesopen) - Molegro (JMedChem) - simbios - simbiosEhits - EhitsBest - 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 Flex (Lengauer) - Glide - EHITS - SPROUT - SPROUT - newlead - newlead - leadfinding - BDTautodockautomator - Cidrux - GDB - 3DFS - quantum - haddock - zdock - escher - rosetta - plants -
Virtual Screening: AutodockScreening - DovisScreening - pocketmatch - pocketmatch -
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 -

Binding Interactions - go to biochem page

Drug Design

Success Stories: Ulcers -

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

Drug Design Software: rasse - LigandBuilder - Sprout - sprout molec design - Autobuild - Ligandscout - wvu -
compound libraries generation from molecular fragment files: inteligand -

Alignment: FBSS - PowerFit, SEAL - FlexS -

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 -

Molecular Diversity

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

Quantum/ab Initio

Tutorials:CCM - qcii - ICC - Cramer - 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 -

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 -
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 -
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 -
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 - 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 - demon key dft metals - demonkey - muenster - turbomol -

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 to calc ESP charges - Vcharge -

Molecule Building: xiangjun 3dna - Beveridge -

Allen & Tildesey's "Computer Simulations in Liquids": CCP5 lipids - CCP5 lipids - CCP5 lipids - CCP5 lipids - CCP5 lipids -
Membrane: Heller - Heller - umass -
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 -
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 -

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 ([email protected]).
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 - CCL - AM-Galaxy - scitech catalog - Deumens links - Interprobe - yasara - chem&mbio - Thakkar suggested software -

ChemKey demo

CAS/Mime definitions

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 -

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

SMILES test structures:
Hexahelicene c1ccc2ccc3ccc4ccc5ccc6ccccc6c5c4c3c2c1
Nonahelicene c1ccc2ccc3ccc4ccc5ccc6ccc7ccc8ccc9ccccc9c8c7c6c5c4c3c2c1
Polyacetylene C=C-C#C-C#C-C=C
SMILES tutorials: pomona - pomona - 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 -
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) -

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 - molgeo - smi23d - smi23d - cubic - weblab - CLiDE SimBioSys - OSRA - acd3D ISISIsis(acd) - Comspec3D - Cybermol - ACD3D - scan2D>3D - Kekule - chemOCR -
3D->2D Convert: GifCreatorNCI(smiles/mol>gif) - GifCreatorErl - GifCreatorErl - GifCreatorErl - interchem - CDK - draw2d - ChemaxonMolConverter - openbabel convert to SMILES and then Xdrawchem input and save - MarvinBeans - ChemDevelopKit - MolConverterMarvin - JChemPaint - OghamOpenEye - rajarshiSDF2JPG -
CactvsErl - xemistry -
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 -
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) -
Compound libraries: asinex - ChemNavigator(sobear11j) -

Chem Database: JChemBase - JChemBase - acdChemfolder - Chemaxon - CambridgeChemfinder - Daylight - MOE - sMol Explorer - Tripos - MDL - Synopsys - Maybridge -

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 -

Compound Libraries: Biospecs - 200k chemstar compounds for screening; SDf (chembase, isis, maccs) format -

Synthesis & reaction: chemkey - koen - unl - syntree - syngen - syngen - spurt - Jorgenson'sCameo - Cameo - holowin - lhasa - synchem - wodca - dendral - 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 -


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


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