Publications

Books

• Molecular Interaction Fields (Cruciani, G., ed.), 2005, Wiley

Reviews

• Cross S, Cruciani G. Molecular fields in drug discovery: getting old or reaching maturity? Drug Discovery Today. 2010 Jan;15(1-2):23-32

GRID

• Käsnänen H, Myllymäki MJ, Minkkilä A, Kataja AO, Saario SM, Nevalainen T, Koskinen AM, Poso A. 3-Heterocycle-phenyl N-alkylcarbamates as FAAH inhibitors: design, synthesis and 3D-QSAR studies. ChemMedChem. 2010 Feb 1;5(2):213-31.
• Nicolotti O, Giangreco I, Miscioscia TF, Carotti A. Improving quantitative structure-activity relationships through multiobjective optimization. J Chem Inf Model. 2009 Oct;49(10):2290-302.
• Musmuca I, Simeoni S, Caroli A, Ragno R. Small-molecule interferon inducers. Toward the comprehension of the molecular determinants through ligand-based approaches. J Chem Inf Model. 2009 Jul;49(7):1777-86.
• • Falchi F, Manetti F, Carraro F, Naldini A, Maga G, Crespan E, Schenone S, Bruno O, Brullo C, Botta M. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors. ChemMedChem. 2009 Jun;4(6):976-87.
  • Tintori C, Magnani M, Schenone S, Botta M. Docking, 3D-QSAR studies and in silico ADME prediction on c-Src tyrosine kinase inhibitors. Eur J Med Chem. 2009 Mar;44(3):990-1000.
  • Caron G, Nurisso A, Ermondi G. How to extend the use of grid-based interaction energy maps from chemistry to biotopics. ChemMedChem. 2009 Jan;4(1):29-36.
  • Salum LB, Polikarpov I, Andricopulo AD. Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity. J Chem Inf Model. 2008 Nov;48(11):2243-53.
  • Nicolotti O, Miscioscia TF, Carotti A, Leonetti F, Carotti A. An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors. J Chem Inf Model. 2008 Jun;48(6):1211-26.
  • Harpsøe K, Liljefors T, Balle T. Prediction of the binding mode of biarylpropylsulfonamide allosteric AMPA receptor modulators based on docking, GRID molecular interaction fields and 3D-QSAR analysis. J Mol Graph Model. 2008 Jan;26(5):874-83.
  • Sciabola S, Carosati E, Cucurull-Sanchez L, Baroni M, Mannhold R. Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes:comparison versus other 2D- and 3D-descriptors. Bioorg Med Chem. 2007 Oct 1;15(19):6450-62.
  • Sísa M, Vilaplana-Polo M, Ballesteros CB, Kohout L. Brassinolide activities of 2alpha,3alpha-diols versus 3alpha,4alpha-diols in the bean second internode bioassay: explanation by molecular modeling methods. Steroids. 2007 Oct;72(11-12):740-50.
  • Guan P, Doytchinova IA, Flower DR. The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. Methods Mol Biol. 2007;409:143-54.
  • Neves MA, Dinis TC, Colombo G, Sá e Melo ML. Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols. ChemMedChem. 2007 Dec;2(12):1750-62.
  • Guan P, Doytchinova IA, Flower DR. The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. Methods Mol Biol. 2007;409:143-54.
  • Montanari ML, Cass QB, Leitão A, Andricopulo AD, Montanari CA. The role of molecular interaction fields on enantioselective and nonselective separation of chiral sulfoxides. J Chromatogr A. 2006 Jul 14;1121(1):64-75.
  • Menezes IR, Leitão A, Montanari CA. Three-dimensional models of non-steroidal ligands: a comparative molecular field analysis. Steroids. 2006 Jun;71(6):417-28.
  • Audouze K, Nielsen EØ, Olsen GM, Ahring P, Jørgensen TD, Peters D, Liljefors T, Balle T. New ligands with affinity for the alpha4beta2 subtype of nicotinic acetylcholine receptors. Synthesis, receptor binding, and 3D-QSAR modeling. J Med Chem. 2006 Jun 1;49(11):3159-71.
  • Ragno R, Simeoni S, Valente S, Massa S, Mai A. 3-D QSAR studies on histone deacetylase inhibitors. A GOLPE/GRID approach on different series of compounds. J Chem Inf Model. 2006 May-Jun;46(3):1420-30.
  • Pirard B, Matter H. Matrix metalloproteinase target family landscape: a chemometrical approach to ligand selectivity based on protein binding site analysis. J Med Chem. 2006 Jan 12;49(1):51-69.
  • Sciabola S, Alex A, Higginson PD, Mitchell JC, Snowden MJ, Morao I. Theoretical prediction of the enantiomeric excess in asymmetric catalysis. An alignment-independent molecular interaction field based approach. J Org Chem. 2005 Oct 28;70(22):9025-7.
  • Vulpetti A, Crivori P, Cameron A, Bertrand J, Brasca MG, D'Alessio R, Pevarello P. Structure-based approaches to improve selectivity: CDK2-GSK3beta binding site analysis. J Chem Inf Model. 2005 Sep-Oct;45(5):1282-90.
  • Asikainen AH, Ruuskanen J, Tuppurainen KA. Alternative QSAR models for selected estradiol and cytochrome P450 ligands: comparison between classical, spectroscopic, CoMFA and GRID/GOLPE methods. SAR QSAR Environ Res. 2005 Dec;16(6):555-65.
  • Korhonen LE, Rahnasto M, Mähönen NJ, Wittekindt C, Poso A, Juvonen RO, Raunio H. Predictive three-dimensional quantitative structure-activity relationship of cytochrome P450 1A2 inhibitors. J Med Chem. 2005 Jun 2;48(11):3808-15.
  • Gratteri P, Bonaccini C, Melani F. Searching for a reliable orientation of ligands in their binding site: comparison between a structure-based (Glide) and a ligand-based (FIGO) approach in the case study of PDE4 inhibitors. J Med Chem. 2005 Mar 10;48(5):1657-65.
  • Ragno R, Artico M, De Martino G, La Regina G, Coluccia A, Di Pasquali A, Silvestri R. Docking and 3-D QSAR studies on indolyl aryl sulfones. Binding mode exploration at the HIV-1 reverse transcriptase non-nucleoside binding site and design of highly active N-(2-hydroxyethyl)carboxamide and N-(2-hydroxyethyl)carbohydrazide derivatives. J Med Chem. 2005 Jan 13;48(1):213-23.
  • Debnath AK. Application of 3D-QSAR techniques in anti-HIV-1 drug design - an overview. Curr Pharm Des. 2005;11(24):3091-110.
  • Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC. Comparative structural and energetic analysis of WW domain-peptide interactions. J Mol Biol. 2004 Nov 26;344(3):865-81.
  • Afzelius L, Raubacher F, Karlén A, Jørgensen FS, Andersson TB, Masimirembwa CM, Zamora I. Structural analysis of CYP2C9 and CYP2C5 and an evaluation of commonly used molecular modeling techniques. Drug Metab Dispos. 2004 Nov;32(11):1218-29.
  • Carosati E, Sciabola S, Cruciani G. Hydrogen bonding interactions of covalently bonded fluorine atoms: from crystallographic data to a new angular function in the GRID force field. J Med Chem. 2004 Oct 7;47(21):5114-25.
  • Braiuca P, Cruciani G, Ebert C, Gardossi L, Linda P. An innovative application of the "flexible" GRID/PCA computational method: study of differences in selectivity between PGAs from Escherichia coli and a Providentia rettgeri mutant. Biotechnol Prog. 2004 Jul-Aug;20(4):1025-31.
  • Audouze K, Nielsen EØ, Peters D. New series of morpholine and 1,4-oxazepane derivatives as dopamine D4 receptor ligands: synthesis and 3D-QSAR model. J Med Chem. 2004 Jun 3;47(12):3089-104.
  • Staerk D, Skole B, Jørgensen FS, Budnik BA, Ekpe P, Jaroszewski JW. Isolationof a library of aromadendranes from Landolphia dulcis and its characterization using the VolSurf approach. J Nat Prod. 2004 May;67(5):799-805.
  • Cruciani G, Benedetti P, Caltabiano G, Condorelli DF, Fortuna CG, Musumarra G. Structure-based rationalization of antitumor drugs mechanism of action by a MIF approach. Eur J Med Chem. 2004 Mar;39(3):281-9.
  • Costi R, Santo RD, Artico M, Massa S, Ragno R, Loddo R, La Colla M, Tramontano E, La Colla P, Pani A. 2,6-Bis(3,4,5-trihydroxybenzylydene) derivatives of cyclohexanone: novel potent HIV-1 integrase inhibitors that prevent HIV-1 multiplication in cell-based assays. Bioorg Med Chem. 2004 Jan 2;12(1):199-215.
  • Tervo AJ, Nyrönen TH, Rönkkö T, Poso A. A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods. J Comput Aided Mol Des. 2003 Dec;17(12):797-810.
  • Ji H, Li H, Flinspach M, Poulos TL, Silverman RB. Computer modeling of selective regions in the active site of nitric oxide synthases: implication for the design of isoform-selective inhibitors. J Med Chem. 2003 Dec 18;46(26):5700-11.
  • Bröer BM, Gurrath M, Höltje HD. Molecular modelling studies on the ORL1-receptor and ORL1-agonists. J Comput Aided Mol Des. 2003 Nov;17(11):739-54.
  • Pirard B. Peroxisome proliferator-activated receptors target family landscape: a chemometrical approach to ligand selectivity based on protein binding site analysis. J Comput Aided Mol Des. 2003 Nov;17(11):785-96.
  • Braiuca P, Ebert C, Fischer L, Gardossi L, Linda P. A homology model of penicillin acylase from Alcaligenes faecalis and in silico evaluation of its selectivity. Chembiochem. 2003 Jul 7;4(7):615-22.
  • Balle T, Andersen K, Søby KK, Liljefors T. Alpha(1) adrenoceptor subtype selectivity. 3D-QSAR models for a new class of alpha(1) adrenoceptor antagonists derived from the novel antipsychotic sertindole. J Mol Graph Model. 2003 Jun;21(6):523-34.
  • Myshkin E, Wang B. Chemometrical classification of ephrin ligands and Eph kinases using GRID/CPCA approach. J Chem Inf Comput Sci. 2003 May-Jun;43(3):1004-10.
  • Jørgensen AT, Sørensen MD, Björkling F, Liljefors T. Binding of alpha-hydroxy-beta-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions. J Comput Aided Mol Des. 2003 May-Jun;17(5-6):383-97.
  • Menezes IR, Lopes JC, Montanari CA, Oliva G, Pavão F, Castilho MS, Vieira PC, Pupo MT. 3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi. J Comput Aided Mol Des. 2003 May-Jun;17(5-6):277-90.
  • Kurz M, Brachvogel V, Matter H, Stengelin S, Thüring H, Kramer W. Insights into the bile acid transportation system: the human ileal lipid-binding protein-cholyltaurine complex and its comparison with homologous structures. Proteins. 2003 Feb 1;50(2):312-28.
  • Sippl W. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods. Bioorg Med Chem. 2002 Dec;10(12):3741-55.
  • Sheridan RP, Holloway MK, McGaughey G, Mosley RT, Singh SB. A simple method for visualizing the differences between related receptor sites. J Mol Graph Model. 2002 Dec;21(3):217-25.
  • Sippl W. Development of biologically active compounds by combining 3D QSAR and structure-based design methods. J Comput Aided Mol Des. 2002 Nov;16(11):825-30.
  • Carrieri A, Carotti A, Barreca ML, Altomare C. Binding models of reversible inhibitors to type-B monoamine oxidase. J Comput Aided Mol Des. 2002 Nov;16(11):769-78.
  • Stoll F, Liesener S, Hohlfeld T, Schrör K, Fuchs PL, Höltje HD. Pharmacophore definition and three-dimensional quantitative structure-activity relationship study on structurally diverse prostacyclin receptor agonists. Mol Pharmacol. 2002 Nov;62(5):1103-11.
  • Terp GE, Cruciani G, Christensen IT, Jørgensen FS. Structural differences of matrix metalloproteinases with potential implications for inhibitor selectivity examined by the GRID/CPCA approach. J Med Chem. 2002 Jun 20;45(13):2675-84.
  • Naumann T, Matter H. Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes. J Med Chem. 2002 Jun 6;45(12):2366-78.
  • Brea J, Rodrigo J, Carrieri A, Sanz F, Cadavid MI, Enguix MJ, Villazón M, Mengod G, Caro Y, Masaguer CF, Raviña E, Centeno NB, Carotti A, Loza MI. New serotonin 5-HT(2A), 5-HT(2B), and 5-HT(2C) receptor antagonists: synthesis, pharmacology, 3D-QSAR, and molecular modeling of (aminoalkyl)benzo and heterocycloalkanones. J Med Chem. 2002 Jan 3;45(1):54-71.
  • Jäger R, Kast SM. Fast prediction of hydration free energies from molecular interaction fields. J Mol Graph Model. 2001;20(2):123-31.
  • Ridderström M, Zamora I, Fjellström O, Andersson TB. Analysis of selective regions in the active sites of human cytochromes P450, 2C8, 2C9, 2C18, and 2C19 homology models using GRID/CPCA. J Med Chem. 2001 Nov 22;44(24):4072-81.
  • Schappach A, Höltje HD. Molecular modelling of 17 alpha-hydroxylase-17,20-lyase. Pharmazie. 2001 Jun;56(6):435-42.
  • Sippl W, Contreras JM, Parrot I, Rival YM, Wermuth CG. Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors. J Comput Aided Mol Des. 2001 May;15(5):395-410.
  • Stilz HU, Guba W, Jablonka B, Just M, Klingler O, König W, Wehner V, Zoller G. Discovery of an orally active non-peptide fibrinogen receptor antagonist based on the hydantoin scaffold. J Med Chem. 2001 Apr 12;44(8):1158-76.
  • Poso A, Gynther J, Juvonen R. A comparative molecular field analysis of cytochrome P450 2A5 and 2A6 inhibitors. J Comput Aided Mol Des. 2001 Mar;15(3):195-202.
  • Cinone N, Hötje HD, Carotti A. Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands. J Comput Aided Mol Des. 2000 Nov;14(8):753-68.
  • Sippl W. Receptor-based 3D QSAR analysis of estrogen receptor ligands-merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. J Comput Aided Mol Des. 2000 Aug;14(6):559-72. PubMed PMID: 10921772.
  • Kastenholz MA, Pastor M, Cruciani G, Haaksma EE, Fox T. GRID/CPCA: a new computational tool to design selective ligands. J Med Chem. 2000 Aug 10;43(16):3033-44.
  • Fichera M, Cruciani G, Bianchi A, Musumarra G. A 3D-QSAR study on the structural requirements for binding to CB(1) and CB(2) cannabinoid receptors. J Med Chem. 2000 Jun 15;43(12):2300-9.
  • Nielsen SF, Nielsen EO, Olsen GM, Liljefors T, Peters D. Novel potent ligands for the central nicotinic acetylcholine receptor: synthesis, receptor binding, and 3D-QSAR analysis. J Med Chem. 2000 Jun 1;43(11):2217-26.
  • Lozano JJ, Pastor M, Cruciani G, Gaedt K, Centeno NB, Gago F, Sanz F. 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands. J Comput Aided Mol Des. 2000 May;14(4):341-53.
  • Filipponi E, Cecchetti V, Tabarrini O, Bonelli D, Fravolini A. Chemometric rationalization of the structural and physicochemical basis for selective cyclooxygenase-2 inhibition: toward more specific ligands. J Comput Aided Mol Des. 2000 Mar;14(3):277-91.
  • Matter H, Schwab W. Affinity and selectivity of matrix metalloproteinase inhibitors: a chemometrical study from the perspective of ligands and proteins. J Med Chem. 1999 Nov 4;42(22):4506-23.
  • Hilgeroth A, Fleischer R, Wiese M, Heinemann FW. Comparison of azacyclic urea A-98881 as HIV-1 protease inhibitor with cage dimeric N-benzyl 4-(4-methoxyphenyl)-1,4-dihydropyridine as representative of a novel class of HIV-1 protease inhibitors: a molecular modeling study. J Comput Aided Mol Des. 1999 May;13(3):233-42.
  • Nielsen SF, Christensen SB, Cruciani G, Kharazmi A, Liljefors T. Antileishmanial chalcones: statistical design, synthesis, and three-dimensional quantitative structure-activity relationship analysis. J Med Chem. 1998 Nov 19;41(24):4819-32.
  • Sippl W, Stark H, Höltje HD. Development of a binding site model for histamine H3-receptor agonists. Pharmazie. 1998 Jul;53(7):433-7.
  • Pastor M, Cruciani G, Watson KA. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis. J Med Chem. 1997 Dec 5;40(25):4089-102.
  • Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors. J Med Chem. 1997 Mar 28;40(7):1136-48.
  • Nilsson J, Wikström H, Smilde A, Glase S, Pugsley T, Cruciani G, Pastor M, Clementi S. GRID/GOLPE 3D quantitative structure-activity relationship study on a set of benzamides and naphthamides, with affinity for the dopamine D3 receptor subtype. J Med Chem. 1997 Mar 14;40(6):833-40.
  • Gouldson PR, Snell CR, Reynolds CA. A new approach to docking in the beta 2-adrenergic receptor that exploits the domain structure of G-protein-coupled receptors. J Med Chem. 1997 Nov 21;40(24):3871-86.
  • Pastor M, Cruciani G. A novel strategy for improving ligand selectivity in receptor-based drug design. J Med Chem. 1995 Nov 10;38(23):4637-47.
  • Watson KA, Mitchell EP, Johnson LN, Cruciani G, Son JC, Bichard CJ, Fleet GW, Oikonomakos NG, Kontou M, Zographos SE. Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection. Acta Crystallogr D Biol Crystallogr. 1995 Jul 1;51(Pt 4):458-72.
  • Cruciani G, Watson KA. Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b. J Med Chem. 1994 Aug 5;37(16):2589-601.
  • Cruciani G, Goodford PJ. A search for specificity in DNA-drug interactions. J Mol Graph. 1994 Jun;12(2):116-29.
  • von Itzstein M, Wu WY, Kok GB, Pegg MS, Dyason JC, Jin B, Van Phan T, Smythe ML, White HF, Oliver SW, et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature. 1993 Jun 3;363(6428):418-23.
  • Wade RC, Goodford PJ. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J Med Chem. 1993 Jan 8;36(1):148-56.
  • Wade RC, Clark KJ, Goodford PJ. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J Med Chem. 1993 Jan 8;36(1):140-7.
  • Wade RC, Molecular Interaction Fields, in 3D QSAR in Drug Design. Theory, methods and Applications (ed. Kubinyi, H). ESCOM, Leiden, 1993 486-505.
  • Nero TL, Wong MG, Oliver SW, Iskander MN, Andrews PR. Aspartate aminotransferase: investigation of the active sites. J Mol Graph. 1990 Jun;8(2):111-5, 92-3.
  • Reynolds CA, Wade RC, Goodford PJ. Identifying targets for bioreductive agents: using GRID to predict selective binding regions of proteins. J Mol Graph. 1989 Jun;7(2):103-8, 100.
  • Boobbyer DN, Goodford PJ, McWhinnie PM, Wade RC. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem. 1989 May;32(5):1083-94.
  • Wade RC, Goodford PJ. The role of hydrogen-bonds in drug binding. Prog Clin Biol Res. 1989;289:433-44.
  • Reynolds CA, Richards WG, Goodford PJ. Introducing selectivity into dihydrofolate reductase inhibitors. Anticancer Drug Des. 1987 Apr;1(4):291-5.
  • Merrett M, Stammers DK, White RD, Wootton R, Kneen G. Characterization of the binding of the anti-sickling compound, BW12C, to haemoglobin. Biochem J. 1986 Oct 15;239(2):387-92.
  • Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 1985 Jul;28(7):849-57.

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GRIND

• Durán A, Zamora I, Pastor M. Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening. J Chem Inf Model. 2009 Sep;49(9):2129-38.
• Durán A, Martínez GC, Pastor M. Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields. J Chem Inf Model. 2008 Sep;48(9):1813-23.
• Kabeya LM, da Silva CH, Kanashiro A, Campos JM, Azzolini AE, Polizello AC, Pupo MT, Lucisano-Valim YM. Inhibition of immune complex-mediated neutrophil oxidative metabolism: a pharmacophore model for 3-phenylcoumarin derivatives using GRIND-based 3D-QSAR and 2D-QSAR procedures. Eur J Med Chem. 2008 May;43(5):996-1007.
• • Ragno R, Simeoni S, Rotili D, Caroli A, Botta G, Brosch G, Massa S, Mai A. Class II-selective histone deacetylase inhibitors. Part 2: alignment-independent GRIND 3-D QSAR, homology and docking studies. Eur J Med Chem. 2008 Mar;43(3):621-32.
  • Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O. hERG classification model based on a combination of support vector machine method and GRIND descriptors. Mol Pharm. 2008 Jan-Feb;5(1):117-27.
  • Larsen SB, Jørgensen FS, Olsen L. QSAR models for the human H(+)/peptide symporter, hPEPT1: affinity prediction using alignment-independent descriptors. J Chem Inf Model. 2008 Jan;48(1):233-41.
  • Sciabola S, Carosati E, Cucurull-Sanchez L, Baroni M, Mannhold R. Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes: comparison versus other 2D- and 3D-descriptors. Bioorg Med Chem. 2007 Oct 1;15(19):6450-62.
  • Menezes IR, Leitão A, Montanari CA. Three-dimensional models of non-steroidal ligands: a comparative molecular field analysis. Steroids. 2006 Jun;71(6):417-28.
  • Crivori P, Reinach B, Pezzetta D, Poggesi I. Computational models for identifying potential P-glycoprotein substrates and inhibitors. Mol Pharm. 2006 Jan-Feb;3(1):33-44.
  • Carosati E, Lemoine H, Spogli R, Grittner D, Mannhold R, Tabarrini O, Sabatini S, Cecchetti V. Binding studies and GRIND/ALMOND-based 3D QSAR analysis of benzothiazine type K(ATP)-channel openers. Bioorg Med Chem. 2005 Oct 1;13(19):5581-91.
  • Vulpetti A, Crivori P, Cameron A, Bertrand J, Brasca MG, D'Alessio R, Pevarello P. Structure-based approaches to improve selectivity: CDK2-GSK3beta binding site analysis. J Chem Inf Model. 2005 Sep-Oct;45(5):1282-90.
  • Cianchetta G, Li Y, Kang J, Rampe D, Fravolini A, Cruciani G, Vaz RJ. Predictive models for hERG potassium channel blockers. Bioorg Med Chem Lett. 2005 Aug 1;15(15):3637-42.
  • Sciabola S, Carosati E, Baroni M, Mannhold R. Comparison of ligand-based and structure-based 3D-QSAR approaches: a case study on (aryl-)bridged 2-aminobenzonitriles inhibiting HIV-1 reverse transcriptase. J Med Chem. 2005 Jun 2;48(11):3756-67.
  • Fontaine F, Pastor M, Zamora I, Sanz F. Anchor-GRIND: filling the gap between standard 3D QSAR and the GRid-INdependent descriptors. J Med Chem. 2005 Apr 7;48(7):2687-94.
  • Cianchetta G, Singleton RW, Zhang M, Wildgoose M, Giesing D, Fravolini A, Cruciani G, Vaz RJ. A pharmacophore hypothesis for P-glycoprotein substrate recognition using GRIND-based 3D-QSAR. J Med Chem. 2005 Apr 21;48(8):2927-35.
  • Gratteri P, Romanelli MN, Cruciani G, Bonaccini C, Melani F. GRIND-derived pharmacophore model for a series of alpha-tropanyl derivative ligands of the sigma-2 receptor. J Comput Aided Mol Des. 2004 May;18(5):361-74.
  • Benedetti P, Mannhold R, Cruciani G, Ottaviani G. GRIND/ALMOND investigations on CysLT1 receptor antagonists of the quinolinyl(bridged)aryl type. Bioorg Med Chem. 2004 Jul 1;12(13):3607-17.
  • Fontaine F, Pastor M, Sanz F. Incorporating molecular shape into the alignment-free Grid-Independent Descriptors. J Med Chem. 2004 May 20;47(11):2805-15.
  • Cruciani G, Benedetti P, Caltabiano G, Condorelli DF, Fortuna CG, Musumarra G. Structure-based rationalization of antitumor drugs mechanism of action by a MIF approach. Eur J Med Chem. 2004 Mar;39(3):281-9.
  • Gutiérrez-de-Terán H, Centeno NB, Pastor M, Sanz F. Novel approaches for modeling of the A1 adenosine receptor and its agonist binding site. Proteins. 2004 Mar 1;54(4):705-15.
  • Crivori P, Zamora I, Speed B, Orrenius C, Poggesi I. Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates. J Comput Aided Mol Des. 2004 Mar;18(3):155-66.
  • Afzelius L, Zamora I, Masimirembwa CM, Karlén A, Andersson TB, Mecucci S, Baroni M, Cruciani G. Conformer- and alignment-independent model for predicting structurally diverse competitive CYP2C9 inhibitors. J Med Chem. 2004 Feb 12;47(4):907-14.
  • Fontaine F, Pastor M, Gutiérrez-de-Terán H, Lozano JJ, Sanz F. Use of alignment-free molecular descriptors in diversity analysis and optimal sampling of molecular libraries. Mol Divers. 2003;6(2):135-47.
  • Afzelius L, Masimirembwa CM, Karlén A, Andersson TB, Zamora I. Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors. J Comput Aided Mol Des. 2002 Jul;16(7):443-58.
  • Cruciani G, Pastor M, Mannhold R. Suitability of molecular descriptors for database mining. A comparative analysis. J Med Chem. 2002 Jun 20;45(13):2685-94.
  • Benedetti P, Mannhold R, Cruciani G, Pastor M. GBR compounds and mepyramines as cocaine abuse therapeutics: chemometric studies on selectivity using grid independent descriptors (GRIND). J Med Chem. 2002 Apr 11;45(8):1577-84.
  • Salamon E, Mannhold R, Weber H, Lemoine H, Frank W. 6-Sulfonylchromenes as highly potent K(ATP)-channel openers. J Med Chem. 2002 Feb 28;45(5):1086-97.
  • Pastor M, Cruciani G, McLay I, Pickett S, Clementi S. GRid-Independent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem. 2000 Aug 24;43(17):3233-43.

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VolSurf

• Fortuna CG, Barresi V, Musumarra G. Design, synthesis and biological evaluation of trans 2-(thiophen-2-yl)vinyl heteroaromatic iodides. Bioorg Med Chem. 2010 May 18.
• Omkvist DH, Larsen SB, Nielsen CU, Steffansen B, Olsen L, Jørgensen FS, Brodin B. A Quantitative Structure-Activity Relationship for Translocation of Tripeptides via the Human Proton-Coupled Peptide Transporter, hPEPT1 (SLC15A1). AAPS J. 2010 May 8.
• Kramer C, Beck B, Clark T. Insolubility classification with accurate prediction probabilities using a MetaClassifier. J Chem Inf Model. 2010 Mar 22;50(3):404-14.
• • Berellini G, Springer C, Waters NJ, Lombardo F. In silico prediction of volume of distribution in human using linear and nonlinear models on a 669 compound data set. J Med Chem. 2009 Jul 23;52(14):4488-95.
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  • Ke YY, Chen YC, Lin TH. Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies. J Comput Chem. 2006 Oct;27(13):1556-70.
  • Ke YY, Lin TH. Modeling the ligand-receptor interaction for a series of inhibitors of the capsid protein of enterovirus 71 using several three-dimensional quantitative structure-activity relationship techniques. J Med Chem. 2006 Jul 27;49(15):4517-25.
  • Doddareddy MR, Cho YS, Koh HY, Kim DH, Pae AN. In silico renal clearance model using classical Volsurf approach. J Chem Inf Model. 2006 May-Jun;46(3):1312-20.
  • de Cerqueira Lima P, Golbraikh A, Oloff S, Xiao Y, Tropsha A. Combinatorial QSAR modeling of P-glycoprotein substrates. J Chem Inf Model. 2006 May-Jun;46(3):1245-54.
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  • Andersen R, Jørgensen FS, Olsen L, Våbenø; J, Thorn K, Nielsen CU, Steffansen B. Development of a QSAR model for binding of tripeptides and tripeptidomimetics to the human intestinal di-/tripeptide transporter hPEPT1. Pharm Res. 2006 Mar;23(3):483-92.
  • Zhuang XM, Xiao JH, Li JT, Zhang ZQ, Ruan JX. A simplified model to predict P-glycoprotein interacting drugs from 3D molecular interaction field. Int J Pharm. 2006 Feb 17;309(1-2):109-14.
  • Korhonen O, Matero S, Poso A, Ketolainen J. Partial least square projections to latent structures analysis (PLS) in evaluating and predicting drug release from starch acetate matrix tablets. J Pharm Sci. 2005 Dec;94(12):2716-30.
  • Almeida TM, Leitão A, Montanari ML, Montanari CA. The molecular retention mechanism in reversed-phase liquid chromatography of meso-ionic compounds by quantitative structure-retention relationships (QSRR). Chem Biodivers. 2005 Dec;2(12):1691-700.
  • Koukoulitsa C, Geromichalos GD, Skaltsa H. VolSurf analysis of pharmacokinetic properties for several antifungal sesquiterpene lactones isolated from Greek Centaurea sp. J Comput Aided Mol Des. 2005 Aug;19(8):617-23.
  • Berellini G, Cruciani G, Mannhold R. Pharmacophore, drug metabolism, and pharmacokinetics models on non-peptide AT1, AT2, and AT1/AT2 angiotensin II receptor antagonists. J Med Chem. 2005 Jun 30;48(13):4389-99.
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  • Caron G, Ermondi G. Calculating virtual log P in the alkane/water system (log P(N)(alk)) and its derived parameters deltalog P(N)(oct-alk) and log D(pH)(alk). J Med Chem. 2005 May 5;48(9):3269-79.
  • Doddareddy MR, Cha JH, Cho YS, Koh HY, Yoo KH, Kim DJ, Pae AN. Volsurf analysis of carbapenem antibiotics. Bioorg Med Chem. 2005 May 16;13(10):3339-49.
  • Crivori P, Zamora I, Speed B, Orrenius C, Poggesi I. Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates. J Comput Aided Mol Des. 2004 Mar;18(3):155-66.
  • Perioli L, Ambrogi V, Bernardini C, Grandolini G, Ricci M, Giovagnoli S, Rossi C. Potential prodrugs of non-steroidal anti-inflammatory agents for targeted drug delivery to the CNS. Eur J Med Chem. 2004 Aug;39(8):715-27.
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  • Staerk D, Skole B, Jørgensen FS, Budnik BA, Ekpe P, Jaroszewski JW. Isolation of a library of aromadendranes from Landolphia dulcis and its characterization using the VolSurf approach. J Nat Prod. 2004 May;67(5):799-805.
  • Cianchetta G, Mannhold R, Cruciani G, Baroni M, Cecchetti V. Chemometric studies on the bactericidal activity of quinolones via an extended VolSurf approach. J Med Chem. 2004 Jun 3;47(12):3193-201.
  • Leitão A, Andricopulo AD, Oliva G, Pupo MT, de Marchi AA, Vieira PC, da Silva MF, Ferreira VF, de Souza MC, Sá MM, Moraes VR, Montanari CA. Structure-activity relationships of novel inhibitors of glyceraldehyde-3-phosphate dehydrogenase. Bioorg Med Chem Lett. 2004 May 3;14(9):2199-204.
  • Kovatcheva A, Golbraikh A, Oloff S, Xiao YD, Zheng W, Wolschann P, Buchbauer G, Tropsha A. Combinatorial QSAR of ambergris fragrance compounds. J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):582-95.
  • Holm R, Hoest J. Successful in silico predicting of intestinal lymphatic transfer. Int J Pharm. 2004 Mar 19;272(1-2):189-93.
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  • Ano R, Kimura Y, Shima M, Matsuno R, Ueno T, Akamatsu M. Relationships between structure and high-throughput screening permeability of peptide derivatives and related compounds with artificial membranes: application to prediction of Caco-2 cell permeability. Bioorg Med Chem. 2004 Jan 2;12(1):257-64.
  • Menezes IR, Lopes JC, Montanari CA, Oliva G, Pavão F, Castilho MS, Vieira PC, Pupo MT. 3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi. J Comput Aided Mol Des. 2003 May-Jun;17(5-6):277-90.
  • Clark DE, Grootenhuis PD. Predicting passive transport in silico-history, hype, hope. Curr Top Med Chem. 2003;3(11):1193-203.
  • Zamora I, Oprea T, Cruciani G, Pastor M, Ungell AL. Surface descriptors for protein-ligand affinity prediction. J Med Chem. 2003 Jan 2;46(1):25-33.
  • Oprea TI, Zamora I, Ungell AL. Pharmacokinetically based mapping device for chemical space navigation. J Comb Chem. 2002 Jul-Aug;4(4):258-66.
  • Ooms F, Weber P, Carrupt PA, Testa B. A simple model to predict blood-brain barrier permeation from 3D molecular fields. Biochim Biophys Acta. 2002 Jul 18;1587(2-3):118-25.
  • Cruciani G, Pastor M, Mannhold R. Suitability of molecular descriptors for database mining. A comparative analysis. J Med Chem. 2002 Jun 20;45(13):2685-94.
  • Tarvainen M, Sutinen R, Somppi M, Paronen P, Poso A. Predicting plasticization efficiency from three-dimensional molecular structure of a polymer plasticizer. Pharm Res. 2001 Dec;18(12):1760-6.
  • Ekins S, Durst GL, Stratford RE, Thorner DA, Lewis R, Loncharich RJ, Wikel JH. Three-dimensional quantitative structure-permeability relationship analysis for a series of inhibitors of rhinovirus replication. J Chem Inf Comput Sci. 2001 Nov-Dec;41(6):1578-86.
  • Rey S, Caron G, Ermondi G, Gaillard P, Pagliara A, Carrupt PA, Testa B. Development of molecular hydrogen-bonding potentials (MHBPs) and their application to structure-permeation relations. J Mol Graph Model. 2001;19(6):521-35, 594-7.
  • Filipponi E, Cruciani G, Tabarrini O, Cecchetti V, Fravolini A. QSAR study and VolSurf characterization of anti-HIV quinolone library. J Comput Aided Mol Des. 2001 Mar;15(3):203-17.
  • Cruciani G, Pastor M, Guba W. VolSurf: a new tool for the pharmacokinetic optimization of lead compounds. Eur J Pharm Sci. 2000 Oct;11 Suppl 2:S29-39.
  • Testa B, Bojarski AJ. Molecules as complex adaptative systems: constrained molecular properties and their biochemical significance. Eur J Pharm Sci. 2000 Oct;11 Suppl 2:S3-14.
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MetaSite

• Boyer D, Bauman JN, Walker DP, Kapinos B, Karki K, Kalgutkar AS. Utility of MetaSite in improving metabolic stability of the neutral indomethacin amide derivative and selective cyclooxygenase-2 inhibitor 2-(1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl)-N-phenethyl-acetamide. Drug Metab Dispos. 2009 May;37(5):999-1008.
• Trunzer M, Faller B, Zimmerlin A. Metabolic soft spot identification and compound optimization in early discovery phases using MetaSite and LC-MS/MS validation. J Med Chem. 2009 Jan 22;52(2):329-35.
• Oh WS, Kim DN, Jung J, Cho KH, No KT. New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism. J Chem Inf Model. 2008 Mar;48(3):591-601.
• • Ahlström MM, Ridderström M, Zamora I, Luthman K. CYP2C9 structure-metabolism relationships: optimizing the metabolic stability of COX-2 inhibitors. J Med Chem. 2007 Sep 6;50(18):4444-52.
  • Sheridan RP, Korzekwa KR, Torres RA, Walker MJ. Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9. J Med Chem. 2007 Jul 12;50(14):3173-84. Epub 2007 Jun 19.
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  • Caron G, Ermondi G, Testa B. Predicting the oxidative metabolism of statins: an application of the MetaSite algorithm. Pharm Res. 2007 Mar;24(3):480-501.
  • Zhou D, Afzelius L, Grimm SW, Andersson TB, Zauhar RJ, Zamora I. Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions. Drug Metab Dispos. 2006 Jun;34(6):976-83.
  • Cruciani G, Carosati E, De Boeck B, Ethirajulu K, Mackie C, Howe T, Vianello R. MetaSite: understanding metabolism in human cytochromes from the perspectiva of the chemist. J Med Chem. 2005 Nov 3;48(22):6970-9.
  • Berellini G, Cruciani G, Mannhold R. Pharmacophore, drug metabolism, and pharmacokinetics models on non-peptide AT1, AT2, and AT1/AT2 angiotensin II receptor antagonists. J Med Chem. 2005 Jun 30;48(13):4389-99.
  • Zamora I, Afzelius L, Cruciani G. Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9. J Med Chem. 2003 Jun 5;46(12):2313-24.

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MoKa

• Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery
  Francesca Milletti and Anna Vulpetti
  J. Chem. Inf. Model., 2010, 50 (6), pp 1062–1074
• Milletti F, Storchi L, Sforna G, Cruciani G. New and original pKa prediction method using grid molecular interaction fields. J Chem Inf Model. 2007 Nov-Dec;47(6):2172-81.
• Milletti F, Storchi L, Sforna G, Cross S, Cruciani G. Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J Chem Inf Model. 2009 Jan;49(1):68-75.
• • Manchester J, Walkup G, Rivin O, You Z. Evaluation of pKa estimation methods on 211 druglike compounds. J Chem Inf Model. 2010 Apr 26;50(4):565-71.
  • Milletti F, Storchi L, Cruciani G. Predicting protein pK(a) by environment similarity. Proteins. 2009 Aug 1;76(2):484-95.
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  • Milletti F, Storchi L, Goracci L, Bendels S, Wagner B, Kansy M, Cruciani G. Extending pKa prediction accuracy: high-throughput pKa measurements to understand pKa modulation of new chemical series. Eur J Med Chem. 2010 Sep;45(9):4270-9.

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SHOP

• Bergmann R, Liljefors T, Sørensen MD, Zamora I. SHOP: receptor-based Scaffold HOPping by GRID-based similarity searches. J Chem Inf Model. 2009 Mar;49(3):658-69.
• Fontaine F, Cross S, Plasencia G, Pastor M, Zamora I. SHOP: a method for structure-based fragment and scaffold hopping. ChemMedChem. 2009 Mar;4(3):427-39.
• Bergmann R, Linusson A, Zamora I. SHOP: scaffold HOPping by GRID-based similarity searches. J Med Chem. 2007 May 31;50(11):2708-17. Epub 2007 May 10.
• • Ahlström MM, Ridderström M, Luthman K, Zamora I. Virtual screening and scaffold hopping based on GRID molecular interaction fields. J Chem Inf Model. 2005 Sep-Oct;45(5):1313-23.

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• Artese A, Cross S, Costa G, Distinto S, Parrotta L, Alcaro S, Ortuso F, Cruciani G. Molecular interaction fields in drug discovery: recent advances and future perspectives. WIREs Comput Mol Sci 2013, 3:594-613.
• Sirci F, Istyastono E P, Vischer H F, Kooistra A J, Nijmeijer S, Kuijer M, Wijtmans M, Mannhold R, Leurs R, de Esch I J P, de Graaf C, Virtual fragment screening: Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints. J. Chem. Inf. Model. 2012, 52(12), pp 3308-3324.
• Cross S, Baroni M, Goracci L, and Cruciani G. GRID-Based Three-Dimensional Pharmacophores I: FLAPpharm, a Novel Approach for Pharmacophore Elucidation. J. Chem. Inf. Model. 2012, 52(10):2587-2598.
• • Cross S, Ortuso F, Baroni M, Costa G, Distinto S, Moraca F, Alcaro S, and Cruciani G. GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods. J. Chem. Inf. Model. 2012, 52(10):2599-2608.
  • Sirci F, Goracci L, Rodriguez D, van Muijlwijk-Koezen J, Gutierrez-de-Teran H, and Mannhold R. Ligand-, structure- and pharmacophore-based molecular fingerprints; a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists. J Comput Aided Mol Des 2012.
  • Brincat JP, Carosati E, Sabatini S, Manfroni G, Fravolini A, Raygada JL, Patel D, Kaatz GW, and Cruciani G. Discovery of Novel Inhibitors of the NorA Multidrug Transporter of Staphylococcus Aureus. J. Med. Chem., 2011, 54 (1), pp 354–365.
  • Carosati E, Sforna G, Pippi M, Marverti G, Ligabue A, Guerrieri D, Piras S, Guaitoli G, Luciani R, Costi MP, and Cruciani G. Ligand-based virtual screening and ADME-tox guided approach to identify triazolo-quinoxalines as folate cycle inhibitors. Bioorg Med Chem 2010, 18 (22), pp 7773-7785.
  • Cross S, Baroni M, Carosati E, Benedetti P and Clementi S. FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set. J. Chem. Inf. Model., 2010, 50 (8), pp 1442–1450
  • Cross S, Cruciani G. Grid-derived structure-based 3D pharmacophores and their performance compared to docking. Drug Discovery Today: Technologies. Volume 7, Issue 4, Winter 2010, Pages e213-e219
  • Sciabola S, Stanton RV, Mills JE, Flocco MM, Baroni M, Cruciani G, Perruccio F, Mason JS. High-throughput virtual screening of proteins using GRID molecular interaction fields. J Chem Inf Model. 2010 Jan;50(1):155-69.
  • Carosati E, Budriesi R, Ioan P, Ugenti MP, Frosini M, Fusi F, Corda G, Cosimelli B, Spinelli D, Chiarini A, Cruciani G. Discovery of novel and cardioselective diltiazem-like calcium channel blockers via virtual screening. J Med Chem. 2008 Sep 25;51(18):5552-65.
  • Baroni M, Cruciani G, Sciabola S, Perruccio F, Mason JS. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. J Chem Inf Model. 2007 Mar-Apr;47(2):279-94.
  • Carosati E, Mannhold R, Wahl P, Hansen JB, Fremming T, Zamora I, Cianchetta G, Baroni M. Virtual screening for novel openers of pancreatic K(ATP) channels. J Med Chem. 2007 May 3;50(9):2117-26. Epub 2007 Apr 11.

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Pentacle

• Giuseppe Ermondi, Giulia Caron, Isela Garcia Pintos, Michela Gerbaldo, Manuel Pérez, Daniel I. Pérez, Zoila Gándara, Ana Martínez, Generosa Gómez, Yagamare Fall. An application of two MIFs-based tools (Volsurf+ and Pentacle) to binary QSAR: The case of a palinurin-related data set of non-ATP competitive Glycogen Synthase Kinase 3β (GSK-3β) inhibitors. Eur j Med Chem. IN PRESS.
• Patrizia Crivori, Giulia Pennella, Miriam Magistrelli, Pietro Grossi†, Anna Maria Giusti. Predicting Myelosuppression of Drugs from in Silico Models. J Chem Inf Model. 2011 Jan. Article ASAP.
• Cristian Obiol-Pardo, Julio Gomis-Tena, Ferran Sanz, Javier Saiz, Manuel Pastor. A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity. J Chem Inf Model. 2011 Jan 20. [Epub ahead of print]
• • Yaziji V, Rodríguez D, Gutiérrez-de-Terán H, Coelho A, Caamaño O, García-Mera X, Brea J, Loza MI, Cadavid MI, Sotelo E. Pyrimidine Derivatives as Potent and Selective A(3) Adenosine Receptor Antagonists. J. Med. Chem., 2011, 54 (2), pp 457–471. Epub 2010 Dec 27
  • Durán A, Zamora I, Pastor M. Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening. J Chem Inf Model. 2009 Sep;49(9):2129-38.
  • Durán A, Martínez GC, Pastor M. Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields. J Chem Inf Model. 2008 Sep;48(9):1813-23.

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