SOARING BEAR Ph.D. Pharmacology
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Scientific advisor to the health professions &
herbal industry
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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
- GregoretUCSC - BirkbeckPPS
- 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)
-
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
-
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 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 -
terms - Alchemist - links - Trygg - wiley - eigenvector - NAmICS - Russian - muni - chemint -
HyperSpin
- HyperSpin
- BOSS/MCPRO
Monte Carlo (Jorgensen) - Monte
Carlo -
Monte Carlo: QMCMOL -
QMCBEAVER - CHAMP
- ZORI - CASINO
-
Conformer Generation: smog
conformer gen - ConCOORDconformgen
- Verachem -
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
-
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
-
NIH Molec Modeling -
Molecular modeling in Education: NetScience
- MacKerell
- Cousins - Boyd
- ICC - PCdemos
- martindale
- SimChemistry
- ccp2 continuum - Steinbach
- Savary - ContinuumElectrostatics(Gilson)
- cache links
- ucsbKahn -
diversity forum - 7/97 conf -
Gronigen: Condensed
Phase-deVries - Solvation
& Dispersion-deVries -
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
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 -
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 -
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
-
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 - Visualize - Molecules-3D - BioCoRe - MOLDYN neutron scattering MD - linux4chemistry 24 programs - linux4chemistry - tinker dynamics (fortran) -
Software descriptions: claessen - netsci - 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 -
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)
- Babeltutorial - openBabel(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 ISIS -
Isis(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