Tag cheminformatics [at least 200 articles] Export

Recent papers classified by the tag cheminformatics.

	The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows [My Copy] Future Generation Computer Systems, Vol. 25, No. 5. (May 2009), pp. 561-567. by David De Roure, Carole Goble, Robert Stevens posted to workflow web20 myexperiment cheminformatics bsl bioclipse by egonw on 2009-11-13 11:48:43 as along with 5 people brianb downhomekitty druvus dullhunk fgibson
	Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (30 October 0000), 091030094710018. by Zsolt Lepp, Chunfei Huang, Takashi Okada posted to similarity nov09 network molecule ligand compound_libraries cheminformatics by nickolay on 2009-11-03 20:39:55 as along with 1 person massivemayhem
	Knowledge-Based Approach to de Novo Design Using Reaction Vectors [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 5. (22 May 2009), pp. 1163-1184. by Hina Patel, Michael J. Bodkin, Beining Chen, Valerie J. Gillet posted to workflow knowledge drug design cheminformatics by nicklynch on 2009-10-26 13:22:32 as along with 1 person alfons
	"Good Annotation Practice" for Chemical Data in Biology [My Copy] In Silico Biology, Vol. 7, No. 0. (1 January 2007), pp. 45-56. by Kirill Degtyarenko, Marcus Ennis, John S. Garavelli posted to kirill-degtyarenko cites-chebi cheminformatics chebi by dullhunk on 2009-10-19 14:45:08 as
	Proteochemometric modeling of HIV protease susceptibility [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (10 April 2008), 181. by Maris Lapins, Martin Eklund, Ola Spjuth, Peteris Prusis, Jarl Wikberg posted to virus qsar proteochemometrics hiv_protease hiv chemometrics cheminformatics by egonw on 2009-10-12 06:08:08 as along with 1 person joseph_x_zhou
	Chemical inference. 3. Formalization of the language of relational chemistry: ontology and algebra [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 28, No. 2. (1 May 1988), pp. 100-115. by John E. Gordon posted to reasoning ontology cheminformatics by egonw on 2009-10-11 10:08:38 as along with 2 people pauldobson dullhunk
	An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 8. (24 August 2009), pp. 1866-1870. by Pierre Baldi, Daniel S. Hirschberg posted to tanimoto similarity oct09 ligand cheminformatics by nickolay on 2009-10-07 01:36:53 as
	Physicochemical Properties of Antibacterial Compounds: Implications for Drug Discovery [My Copy] Journal of Medicinal Chemistry, Vol. 51, No. 10. (1 May 2008), pp. 2871-2878. by Rosemarie O’Shea, Heinz E. Moser posted to fragment cheminformatics by mnishimu on 2009-10-06 07:18:54 as
	Network analysis of FDA approved drugs and their targets. [My Copy] The Mount Sinai journal of medicine, New York, Vol. 74, No. 1. (April 2007), pp. 27-32. by Avi Ma'ayan, Sherry L. Jenkins, Joseph Goldfarb, Ravi Iyengar posted to network fda drug discovery cheminformatics by egonw on 2009-09-21 07:53:54 as along with 2 people and 1 group guhjy raiyar steinmetzlab
	Predicting drug side-effects by chemical systems biology. [My Copy] Genome biology, Vol. 10, No. 9. (2009), 238. by Nicholas P. Tatonetti, Tianyun Liu, Russ B. Altman posted to systems-biology cheminformatics by peterli on 2009-09-16 13:13:46 as along with 4 people flbarroso Yanno abhishek_tiwari biomcgary
	SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 28, No. 1. (1 February 1988), pp. 31-36. by David Weininger posted to smiles cheminformatics by egonw on 2009-09-06 21:29:11 as along with 6 people npt11tpn mkayala nanonan higueruelo schwartzjmc LamBras
	Small Molecule Subgraph Detector (SMSD) toolkit [My Copy] Journal of Cheminformatics, Vol. 1, No. 1. (2009), 12. by Syed A. Rahman, Matthew Bashton, Gemma Holliday, Rainer Schrader, Janet Thornton posted to cheminformatics by cdsouthan on 2009-08-30 21:12:55 as along with 3 people and 1 group ucbcjbm reyez grottenolm Journal picks
	MolDIA: XML based system of molecular diversity analysis towards virtual screening and QSPR. [My Copy] SAR and QSAR in environmental research, Vol. 17, No. 1. (February 2006), pp. 11-23. by A. G. Maldonado, M. Petitjean, J-P P. Doucet, A. Panaye, B. T. Fan posted to xml cheminformatics by egonw on 2009-08-29 19:46:01 as
	Supervised Self-Organizing Maps in Crystal Property and Structure Prediction [My Copy] Crystal Growth & Design, Vol. 7, No. 9. (1 September 2007), pp. 1738-1745. by E. L. Willighagen, R. Wehrens, W. Melssen, R. de Gelder, L. M. C. Buydens posted to supervised som papers kohonen crystallography chemometrics chemistry cheminformatics by egonw on 2009-08-27 13:04:56 as
	Metric Validation and the Receptor-Relevant Subspace Concept [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 39, No. 1. (1 January 1999), pp. 28-35. by R. S. Pearlman, K. M. Smith posted to qsar descriptors cheminformatics bcut by egonw on 2009-08-26 22:28:18 as
	Workflow based framework for life science informatics [My Copy] Computational Biology and Chemistry, Vol. 31, No. 5-6. (October 2007), pp. 305-319. by Abhishek Tiwari, Arvind K. T. Sekhar posted to cheminformatics by egonw on 2009-08-26 21:01:18 as along with 10 people and 1 group abhishek_tiwari operon pekrau andrewclegg Thaverkamp druvus zufar nicklynch guhjy moborg Orengo Group Journal Picks
	CREDO: A Protein–Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to chemistry_database cheminformatics by richardbickerton on 2009-08-26 11:59:39 as along with 6 people mijam pansapiens bicko nanonan massivemayhem higueruelo
	Complementarity between public and commercial databases: new opportunities in medicinal chemistry informatics. [My Copy] Curr Top Med Chem, Vol. 7, No. 15. (2007), pp. 1502-1508. by C. Southan, P. Várkonyi, S. Muresan posted to emot drug database cheminformatics by jmuhlich on 2009-08-24 20:55:58 as along with 3 people sorelmuresan richardbickerton kuhn
	Prediction of Physicochemical Parameters by Atomic Contributions [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 39, No. 5. (1 September 1999), pp. 868-873. by Scott A. Wildman, Gordon M. Crippen posted to smarts cheminformatics by egonw on 2009-08-23 10:22:05 as along with 1 person girschick
	A survey of across-target bioactivity results of small molecules in PubChem [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2251-2255. by Lianyi Han, Yanli Wang, Stephen H. Bryant posted to sep09 cheminformatics bioactivity by nickolay on 2009-08-20 15:55:00 as along with 1 person and 1 group reyez Journal picks
	ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI) [My Copy] Journal of Computer-Aided Molecular Design, Vol. 23, No. 4. (1 April 2009), pp. 195-198. by Wendy Warr posted to wendy-warr john-overington drug-discovery cheminformatics chembl by dullhunk on 2009-08-20 13:12:25 as along with 1 person zimbo1
	Public chemical compound databases. [My Copy] Current opinion in drug discovery & development, Vol. 11, No. 3. (May 2008), pp. 393-404. by A. J. Williams posted to database chemistry cheminformatics by egonw on 2009-08-14 07:19:42 as along with 2 people nicklynch dullhunk
	FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 7. (27 July 2009), pp. 1630-1642. by Peter S. Kutchukian, David Lou, Eugene I. Shakhnovich posted to cheminformatics by nicklynch on 2009-08-05 11:48:49 as along with 2 people nickolay alfons
	Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 1. (1 January 2007), pp. 195-207. by Gilles Marcou, Didier Rognan posted to cheminformatics docking by richardbickerton on 2009-07-30 18:50:13 as along with 8 people RebeccaHamer klexa nanonan BragilMassoud peprovy schlauchi massivemayhem sithmein
	Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 7. (14 April 2009), pp. 836-845. by Pedro J. Ballester, Paul W. Finn, W. Graham Richards posted to cheminformatics virtual_screening by richardbickerton on 2009-07-30 12:41:12 as along with 2 people massivemayhem reyez
	Structural Diversity of Organic Chemistry. A Scaffold Analysis of the CAS Registry [My Copy] The Journal of Organic Chemistry, Vol. 73, No. 12. (1 June 2008), pp. 4443-4451. by Alan H. Lipkus, Qiong Yuan, Karen A. Lucas, et al.Susan A. Funk, William F. Bartelt, Roger J. Schenck, Anthony J. Trippe posted to cheminformatics by richardbickerton on 2009-07-30 12:34:54 as along with 1 person abhishek_tiwari
	Chemical Substructure Search in SQL [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 1. (26 January 2009), pp. 22-27. by Adel Golovin, Kim Henrick posted to cheminformatics by richardbickerton on 2009-07-29 14:51:01 as along with 5 people pauldobson higueruelo dullhunk zimbo1 sschurer
	Carbon-fate maps for metabolic reactions [My Copy] Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3193-3199. by Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek posted to cheminformatics rule by schwartzjmc on 2009-07-27 14:34:16 as along with 1 person hryk
	Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases [My Copy] BMC Medical Genomics, Vol. 2, No. 1. (2009), 2. by Douglas Kell posted to ageing aging als alzheimers atherosclerosis bioinformatics carrier chelation chelators diabetes fenton genotype-phenotype hepcidin iron lcn2 metabolism modelling neurodegeneration nf-kappab nf-kb ngal obesity parkinsons philosophy physiology polyphenols pre-eclampsia preeclampsia statistics systems_biology transporters ligand amd antoimicrobial asbestos asbestosis cancer copd diet gout malaria nash nutrition oncology sepsis sids smoking xenobiotics huntington antioxidant arthritis asthma cardiovascular chemistry damage diease frailty friedreichs_ataxia heart_failure hypertension hypoxia ibd injury longevity lupus metabolic_syndrome prooxidant reperfusion rheumatoid siderophores stroke anti-inflammatory combinatorial cytokines erythropoietin hif inflammation statins cheminformatics lbd mind_map reactive siderocalin taverna alzheimer parkinson rls by dbk on 2009-07-26 22:57:43 as along with 5 people and 6 groups pmendes gemmalholliday cchand dullhunk HEIRS dbk-lab HEIRS Oxidative Stress HEIRS Immunology and Autoimmune Diseases HEIRS Heavy Metal Toxicity HEIRS - Environmental Illness Research HEIRS Cellular Biology
	Small Molecule Shape-Fingerprints [My Copy] Journal of Chemical Information and Modeling, Vol. 45, No. 3. (1 May 2005), pp. 673-684. by James A. Haigh, Barry T. Pickup, J. Andrew Grant, Anthony Nicholls posted to 3d barrypickup cheminformatics fingerprints shape sheffield by pauldobson on 2009-07-17 08:49:53 as
	The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. [My Copy] ChemInform, Vol. 34, No. 21. (2003) by Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen posted to bioinformatics cheminformatics chemoinformatics by Scis0000002 on 2009-06-30 16:41:11 as along with 1 person dullhunk
	Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. [My Copy] Combinatorial chemistry & high throughput screening, Vol. 10, No. 8. (September 2007), pp. 719-731. by A. Bender, D. W. Young, J. L. Jenkins, et al.M. Serrano, D. Mikhailov, P. A. Clemons, J. W. Davies posted to cheminformatics drug-discovery drug_targets by ajaymalik on 2009-06-26 00:05:33 as
	A crowdsourcing evaluation of the NIH chemical probes [My Copy] Nat Chem Biol, Vol. 5, No. 7. (July 2009), pp. 441-447. by Tudor I. Oprea, Cristian G. Bologa, Scott Boyer, et al.Ramona F. Curpan, Robert C. Glen, Andrew L. Hopkins, Christopher A. Lipinski, Garland R. Marshall, Yvonne C. Martin, Liliana Ostopovici-Halip, Gilbert Rishton, Oleg Ursu, Roy J. Vaz, Chris Waller, Herbert Waldmann, Larry A. Sklar posted to bioactivity cheminformatics pubchem by cdsouthan on 2009-06-24 09:28:44 as
	DrugBank: a knowledgebase for drugs, drug actions and drug targets. [My Copy] Nucleic acids research, Vol. 36 (Database issue), No. Database issue. (11 January 2008), pp. D901-D906. by David S. Wishart, Craig Knox, An C. Guo, et al.Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali posted to anti-tnf cheminformatics database drugs_search neutraceutical ra by ajaymalik on 2009-06-23 17:17:11 as along with 8 people and 1 group sjcockell ipark-kaist bertelsen daforerog Scis0000002 guhjy sobolevnrm dullhunk baker-group
	The Characterization of Chemical Structures Using Molecular Properties. A Survey [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 40, No. 2. (1 March 2000), pp. 195-209. by David J. Livingstone posted to cheminformatics mutcar by jxl on 2009-06-23 15:09:45 as along with 1 person Scis0000002
	Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. [My Copy] Chemistry Central journal, Vol. 2 (2008) by N. M. O'Boyle, C. Morley, G. R. Hutchison posted to babel cheminformatics pybel python by ghutchis on 2009-06-12 14:26:20 as along with 3 people Scis0000002 nicklynch massivemayhem
	Comparison of Nonbinary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 5. (22 May 2009), pp. 1193-1201. by Aysha A. Khalifa, Maciej Haranczyk, John Holliday posted to baldi cheminformatics molecules search similarity by kmdaily on 2009-06-08 21:37:37 as
	Cheminformatics analysis and learning in a data pipelining environment. [My Copy] Molecular diversity, Vol. 10, No. 3. (August 2006), pp. 283-299. by Moises Hassan, Robert D. Brown, Shikha Varma-O'brien, David Rogers posted to cheminformatics by schwartzjmc on 2009-05-27 12:39:06 as along with 2 people egonw LamBras
	Similarity-based virtual screening using 2D fingerprints [My Copy] Drug Discovery Today, Vol. 11, No. 23-24. (December 2006), pp. 1046-1053. by P. Willett posted to cheminformatics by schwartzjmc on 2009-05-27 12:38:20 as along with 2 people pimmy Scis0000002
	SMILES. 2. Algorithm for generation of unique SMILES notation [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 29, No. 2. (1 May 1989), pp. 97-101. by David Weininger, Arthur Weininger, Joseph L. Weininger posted to cheminformatics by schwartzjmc on 2009-05-27 12:36:12 as along with 2 people mkayala LamBras
	Cinfony - combining Open Source cheminformatics toolkits behind a common interface. [My Copy] Chemistry Central journal, Vol. 2 (2008) by N. M. O'Boyle, G. R. Hutchison posted to cheminformatics python tools by apaydin on 2009-05-13 12:50:59 as along with 1 person egonw
	SuperSite: dictionary of metabolite and drug binding sites in proteins [My Copy] Nucl. Acids Res. (8 October 2008), gkn618. by Andre, Stefan Gunther, Dominic Jansen, Carolin Heeger, Paul F. Thaben, Robert Preissner posted to cheminformatics database drug emot protein by jmuhlich on 2009-04-10 22:15:40 as along with 5 people and 1 group Effie pauldobson reyez lptolik pengchy NaCTeM
	Chemical Descriptors Library (CDL): A Generic, Open Source Software Library for Chemical Informatics [My Copy] J. Chem. Inf. Model. (20 September 2008) by Vladimir J. Sykora, David E. Leahy posted to cheminformatics open software source by jmuhlich on 2009-04-10 21:41:17 as along with 4 people egonw q_w_e_r_t_y lptolik zimbo1
	‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries [My Copy] Drug Discovery Today, Vol. 14, No. 1-2. (28 January 2009), pp. 31-40. by P. Dobson, Y. Patel, D. Kell posted to cheminformatics drug lipinski metabolite transport by jmuhlich on 2009-04-10 21:25:27 as along with 9 people mingzhi richardbickerton massivemayhem vpenelle lptolik pauldobson sschurer egonw dullhunk
	Some Basic Data Structures and Algorithms for Chemical Generic Programming [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 44, No. 5. (1 September 2004), pp. 1571-1575. by Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu posted to chemical-generic-programming cheminformatics reconstruction rules smarts systems-biology by pauldobson on 2009-04-07 13:42:58 as
	SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 12. (22 December 2008), pp. 2294-2307. by Webster R. Homer, Jon Swanson, Robert J. Jilek, Tad Hurst, Robert D. Clark posted to cheminformatics line-notation reconstruction rules sybyl systems-biology by pauldobson on 2009-04-07 13:39:39 as along with 1 person N-te_Jr
	A Cheminformatic Toolkit for Mining Biomedical Knowledge. [My Copy] Pharm Res (24 March 2007) by Gus R. Rosania, Gordon Crippen, Peter Woolf, David States, Kerby Shedden posted to cheminformatics integration pubchem by svozil to the group Bioinformatics on 2009-04-04 21:50:55 as along with 3 people and 1 group Effie guhjy kuhn NaCTeM
	ChEBI: a database and ontology for chemical entities of biological interest [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D344-350. by Kirill Degtyarenko, Paula de Matos, Marcus Ennis, et al.Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcantara, Michael Darsow, Mickael Guedj, Michael Ashburner posted to cheminformatics by schwartzjmc on 2009-03-16 15:53:03 as along with 11 people and 1 group pauladza guhjy peterli Effie pauldobson richardbickerton anthropomorphism irenas dullhunk massivemayhem grottenolm NaCTeM
	Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 32, No. 3. (1 May 1992), pp. 244-255. by Arthur Dalby, James G. Nourse, Douglas W. Hounshell, et al.Ann K. Gushurst, David L. Grier, Burton A. Leland, John Laufer posted to cheminformatics by schwartzjmc on 2009-03-16 15:51:37 as
	Chemical registries--in the fourth decade of service. [My Copy] Journal of chemical information and computer sciences, Vol. 41, No. 2. (r 2001), pp. 259-263. by R. E. Buntrock posted to cheminformatics by schwartzjmc on 2009-03-16 15:48:07 as

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bioinformatics	18
clustering	17
vhts	15
chemistry	13
similarity	13
database	11
drug	11
chemoinformatics	10
virtual_screening	9
papers	8
baldi	7
docking	7
nlp	7
protein	7
search	7
fingerprint	6
ligand	6
review	6
tanimoto	6
chemdb	5
diversity_selection	5
drug-binding	5
molecules	5
ontology	5
opensource	5
qsar	5
2006	4
chemogenomics	4
computational_chemistry	4
drug_design	4
graph	4
molecular_modelling	4
molecular_query_language	4
mql	4
protein-function	4
protein-structure	4
sar	4
scaffold_hopping	4
binding-site	3
bioactivity	3
biocad	3
chemicalspace	3
chemometrics	3
conformation	3
data	3
drug-discovery	3
drugdesign	3
integration	3
java	3
kinase	3
network	3
pubchem	3
python	3
rules	3
shapes	3
svm	3
systems-biology	3
xml	3
bioclipse	2
cancer	2
cdk	2
chebi	2
chemistry_database	2
classification	2
cml	2
combinatorial_libraries	2
compound_libraries	2
druglike	2
duncanhull	2
emot	2
gochebi	2
graphtheory	2
hts	2
informatics_extraction	2
library_design	2
mining	2
molecule	2
nov09	2
oct09	2
pybel	2
ranking	2
reasoning	2
reconstruction	2
semantic	2
sep09	2
similaritysearch	2
smarts	2
statistics	2
virtualscreening	2
workflow	2
bedroc	1
comfa	1
discovery	1
lipinski	1
metabolite	1
nash	1
nf-kb	1
nmr	1
prediction	1
reactive	1

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