HINT! ® Publications

HINT!® Publications

Allosteric Modifiers of Hemoglobin. 2. Crystallographically Determined Binding Sites and Hydrophobic Binding/Interaction Analysis of Novel Hemoglobin Oxygen Effectors. F.C. Wireko, G.E. Kellogg, and D.J. Abraham, J. Med. Chem. 1991, 34, 758-767.
HINT - A New Method of Empirical Hydrophobic Field Calculation for CoMFA. G.E. Kellogg, S.F. Semus, and D.J. Abraham, J. Computer Aided Mol. Design 1991, 5, 545-552.
New Tools for Modeling and Understanding Hydrophobicity and Hydrophobic Interactions. G.E. Kellogg, G.S. Joshi, and D.J. Abraham, Med. Chem. Res. 1992, 1, 444-453.
KEY, LOCK, and LOCKSMITH. Complementary Hydrophobicity Map Predictions of Drug Structure from a Known Receptor/Receptor Structure from Known Drugs. G.E. Kellogg and D.J. Abraham, J. Mol. Graph. 1992, 10, 212-217.
Crystallographic Refinement and Structure Analysis of the Complex of Wheat Germ Agglutinin with a Bivalent Sialoglycopeptide from Glycophorin A. C.S. Wright and J. Jaeger, J. Mol. Biol. 1993, 232, 620-638.
Hydrophobic Fields. D.J. Abraham and G.E. Kellogg, in "3D QSAR in Drug Design, Theory, Methods and Applications", H. Kubinyi, ed., ESCOM Sciences Publishers BV, Leiden, 1993, pp. 506-522.
Effect of Distamycin on Chlorambucil-Induced Mutagenesis in pZ189: Evidence of a Role for Minor Groove Alkylation at Adenine N-3. P. Wang, G.B. Bauer, G.E. Kellogg, D.J. Abraham, and L.F. Povirk, Mutagenesis 1994, 9, 133-139.
The Effect of Physical Organic Properties on Hydrophobic Fields. D.J. Abraham and G.E. Kellogg, J. Computer Aided Mol. Design (Symposium Proceedings: 1993 Meeting of the Molecular Graphics Society) 1994, 8, 41-49.
Cyclodextrin - Barbiturate Inclusion Complexes: A CoMFA/HINT 3-D QSAR Study. V.R. Nayak and G.E. Kellogg, Med. Chem. Res. 1994, 3, 491-502.
Structural Determinants of High-Affininty Binding of Ryanoids to the Vertebrate Skeletal Muscle Ryanodine Receptor: A Comparative Molecular Field Analysis. W. Welch, S. Ahmad, J.A. Airey, K. Gerzon, R.A. Humerickhouse, H.R. Besch, Jr., L. Ruest, P. Deslongchamps, and J.L. Sutko, Biochem. 1994, 33, 6074-6085.
Evaluating Docked Complexes with the HINT Exponential Function and Empirical Atomic Hydrophobicities. E.C. Meng, I.D. Kuntz, D.J. Abraham, and G.E. Kellogg, J. Computer Aided Mol. Design 1994, 8, 299-306.
3D-QSAR of Human Immunodeficiency Virus (I) Protease Inhibitors. III Interpretation of CoMFA Results. T.I. Oprea, C.L. Waller, and G.R. Marshall, Drug Design and Discovery 1994, 12, 29-51.
A Three Dimensional Technique for the Calculation of Octanol-Water Partition Coefficients. C.L. Waller, Quant. Struct.-Act. Relat. 1994, 13, 172-176.
Interactions at the Alpha1Beta1 Interface in Hemoglobin: A Single Amino Acid Change Affects Dimer Ratio in Transgenic Mice Expressing Human Hemoglobin. S.P. White, P. Birch, and R. Kumar, Hemoglobin 1994, 18, 413-426.
Three-Diemensional Quantitative Structure-Activity Relationships of Dioxins and Dioxin-like Compounds: Model Validation and Ah Receptor Characterization. C.L. Waller and J.D. McKinney, Chem. Res. Toxicol. 1995, 8, 847-858.
Using Three-Dimensional Quantitative Structure-Activity Relationships to Examine Estrogen Receptor Binding Affinities of Polychlorinated Hydroxybiphenyls. C.L. Waller, D.L. Minor, and J.D. McKinney, Environ. Health Persp. 1995, 103, 702-707.
(+)-cis-N-(Para-, Meta-, and Ortho-substituted benzyl)-N-normetazocines: Synthesis and Binding Affinity at the [³H]-(+)-Pentazocine-Labeled (1) Site and Quantitative Structure-Activity Relationship Studies. S.W. Mascarella, X. Bai, W. Williams, B. Sine, W.D. Bowen, and F.I. Carroll, J. Med. Chem. 1995, 38, 565-569.
Structural Basis for Serpin Inhibitor Activity. H.T. Wright and J.N. Scarsdale, Proteins 1995, 22, 210-225.
Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery. E.J. Martin, J.M. Blaney, M.A. Siani, D.C. Spellmeyer, A.K. Wong, and W.H. Moos, J. Med. Chem. 1995, 38, 1431-1436.
Modeling the Cytochrome P450-Mediated Metabolism of Chlorinated Volatile Organic Compounds. C.L. Waller, M.V. Evans, and J.D. McKinney, Drug Metab. Disp. 1996, 24, 203-210.
All-Atom Models for the Non-Nucleoside Binding Site of HIV-1 Reverse Transcriptase Complexed with Inhibitors: A 3D QSAR Approach. R. Gussio, N. Pattabiraman, D.W. Zaharevitz, G.E. Kellogg, I.A. Topol, W.G. Rice, C.A. Schaeffer, J.W. Erickson, and S.K. Burt, J. Med. Chem. 1996, 39, 1645-1650.
VALIDATE: A new method for the receptor-based prediction of binding affinities of Novel Ligands. R.D. Head, M.L. Smyte, T.I. Oprea, C.L. Waller, S.M. Green, and G.R. Marshall, J. Am. Chem. Soc., 1996, 118, 3959-3969.
The Pyrrole Locus is the Major Orienting Factor in Ryanodine Binding. W. Welch, J.L. Sutko, K.E. Mitchell, J. Airey, and L. Ruest, Biochemistry, 1996, 35, 7165-7173.
Differences in Hydropathic Properties of Ligand Binding at four Independent Sites in Wheat Germ Agglutinin-Oligosaccharide Crystal Complexes. C.S. Wright and G.E. Kellogg, Protein Sci., 1996 5, 1466-1476.
Calculation Procedures for Molecular Lipophilicty: A Comparative Study. R. Mannhold and K. Dross, Quant. Struct.-Act. Relat. 1996, 15, 403-409.
Synthesis and anticonvulsant activities of 3,3-dialkyl- and 3-alkyl-3-benzyl-2-piperidinones (delta-valerolactams) and hexahydro-2H-azepin-2-ones (epsilon-caprolactams). P.A. Reddy, K.E. Woodward, S.M. McIlheran, B.C.H. Hsiang, T.N. Latifi, M.W. Hill, S.M. Rothman, J.A. Ferrendilli and D.F. Covey, J. Med. Chem. 1997, 40, 44-49.
Molecular Modeling Study of the Multidrug Resistance Modifiers cis- and trans-Flupentixol. M. Wiese and I.K. Pajeva, Pharmazie 1997, 52, 679-685.
Modeling chemistry, and biology of the benzolactam analogues of indolactam V (ILV) .2. Identification of the binding site of the benzolactams in the CRD2 activator-binding domain of PKC delta and discovery of an ILV analogue of improved isozyme selectivity. A.P. Kozikowski, S. Wang, D. Ma, J. Yao, S. Ahmad, R.I. Glazer, K. Bogi, P. Acs, S. Modarres, N.E. Lewin, P.M. Blumberg, J. Med. Chem. 1997, 40, 1316-1326.
Partition coefficients of fuel system icing inhibitors: Semiempirical molecular orbital calculations. S. Trohalaki and R. Pachter, Energy and Fuels 1997, 11, 647-655.
Hydropathic Analysis of the Non-covalent Interactions between Molecular Subunits of Structurally Characterized Hemoglobins. D.J. Abraham, G.E. Kellogg, J. M. Holt, and G. K. Ackers, J. Mol. Biol. 1997, 272, 613-632.
Effects of Entropy on QSAR Equations for HIV-1 Protease: 1. Using Hydropathic Binding Descriptors. 2. Unrestrained Complex Structure Optimizations. D.T. Wei, J.C. Meadows and G.E. Kellogg, Med. Chem. Res. 1997, 7, 259-270.
Finding Optimum Field Models for 3D QSAR. G.E. Kellogg, Med. Chem. Res. 1997, 7, 417-427.
Unsymmetric nonpeptidic HIV protease inhibitors containing anthranilamide as a P2' ligand. R.S. Randad, L. Lubkowska, M.A. Eissenstat, S.V. Gulnik, B. Yu, T.N. Bhat, D.J. Clanton, T. House, S.F. Stinson and J.W. Erickson, Bioorg. Med. Chem. Lett. 1998, 8, 3537-3542.
Structural differences between antagonist binding sites on GABA receptors of insects and mammals: Approach by 3D-QSAR. M. Akamatsu and Y. Ozoe, J. Pesticide Sci. 1998, 23, 344-348.
Utilization of a 3D QSAR Methodology for Data Mining the National Cancer Institute Respository of Small Molecules in Application to HIV-1 Reverse Transcriptase Inhibition. R. Gussio, N. Pattabiraman, G.E. Kellogg, D.W. Zaharevitz, Methods 1998, 14, 255-263.
Comparative molecular field analysis (CoMFA) of a series of symmetrical bis-benzamide cyclic urea derivatives as HIV-1 protease inhibitors. A.K. Debnath, J. Chem. Info. Comput. Sci. 1998, 38, 761-767.
Molecular modeling studies on binding of bFGF to heparin and its receptor FGFR1, K. Lam, V.S.R. Rao and P.K. Qasba, J. Biomol. Struct. Dynamics 1998, 15, 1009-1027.
Molecular Modeling of Phenothiazines and Related Drugs as Multidrug Resistance Modifiers: A Comparative Molecular Field Analysis Study. I. Pajeva and M. Wiese, J. Med. Chem. 1998, 41, 1815-1826.
Structure/function of allosteric effectors of hemoglobin. D.J. Abraham, J. Kister, G.S. Joshi, F.C. Wireko, M.K. Safo, M.C. Marden and C. Poyart, Med. Chem. Res. 1998, 8, 478-486.
A comparative molecular field analysis of propafenone-type modulators of cancer multidrug resistance. I.K. Pajeva and M. Wiese, Quant. Struct.-Act. Relat. 1998, 17, 301-312.
Quantitative structure-activity studies of insect growth regulators XIV. Three-dimensional quantitative structure-activity relationship of ecdysone agonists including dibenzoylhydrazine analogs. Y. Nakagawa, K. Hattori, B. Shimuzu, M. AKamatsu, H. Miyagawa and T. Ueno, Pesticide Sci. 1998, 53, 267-277.
Identification and Hydropathic Characterization of Structural Features Affecting Sequence Selectivity for Doxorubicin Intercalation into DNA Double-Stranded Polynucleotides. G.E. Kellogg, J.N. Scarsdale, and F.A. Fornari, Nucl. Acids Res. 1998, 26, 4721-4732.
Synthesis and modeling studies of a potent conformationally rigid muscarinic agonist: 1-azabicyclo[2.2.1]heptanespirofuranone. E.S.C. Wu, A. Kover and S.F. Semus, J. Med. Chem. 1998, 41, 4181-4185.
Multivariate analysis of experimental and computational descriptors of molecular lipophilicity. R. Mannhold, G. Cruciani, K. Dross and R. Rekker, J. Computer Aided Mol. Design 1998, 12, 573-581.
Repaglinide and related hypoglycemic benzoic acid derivatives. W. Grell, R. Hurnaus , G. Griss, R. Sauter, E. Rupprecht, M. Mark, P. Luger, H. Nar, H. Wittneben and P. Muller, J. Med. Chem. 1998, 41, 5219-5246.
Ionization Constants and Distribution Coefficients of Phenothiazines and Calcium Channel Antagonists Determined by a pH-metric Method and Correlation with Calculated Partition Coefficients. U. Franke, A. Munke, and M. Wiese, J. Pharm. Sci. 1999, 88, 89-95.
Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes. R. Bursi and P.D.J. Grootenhuis, J. Computer Aided Mol. Design 1999, 13, 221-232.
Three-Dimensional Quantitative Structure-Activity Relationship Study on Cyclic Urea Derivatives as HIV-1 Protease Inhibitors: Application of Comparative Molecular Field Analysis. A.K. Debnath, J. Med. Chem. 1999 42, 249-259.
New QSAR methods applied to structure-activity mapping and combinatorial chemistry. F.R. Burden and D.A. Winkler, J. Chem. Info. Computer Sci. 1999, 39, 236-242.
Investigation of 5-HT4 agonist activities using molecular field analysis. M.N. Iskander, I.M. Coupan and D.A. Winkler, J. Chem. Soc. Perk. Trans. 2 1999, 153-158.
Molecular modeling of the hypoxia-inducible factor-1 (HIF-1). G. Michel, E. Minet, I. Ernest, F. Durant, J. Remacle and C. Michiels, Theor. Chem. Acc. 1999, 101, 51-56.
Development of Empirical Biomolecular Interaction Models that Incorporate Hydrophobicity and Hydropathy. The HINT Paradigm. G.E. Kellogg and D.J. Abraham, ANALUSIS 1999, 27, 19-22.
3-D Pharmacophore Analysis of Aldose Reductase Inhibitory Spiroquinazolinones. K. Nakao, M. Asao, H. Shirai and R. Shimuzu, Drug Design and Discovery (in press).
Probing the Binding of Indolactam-V to Protein Kinase C through Site-Directed Mutagenesis and Computational Docking Simulations. S. Wang, M. Liu, N.E. Lewin, P.S. Lorenzo, D. Bhattacharrya, L. Quiao, A.P. Kozikowski and P.M. Blumberg, J. Med. Chem. 1999, 42, 3436-3446.
Crystal Structure of Rabbit Cytosolic Serine Hydroxymethyltransferase at 2.8 Å Resolution: Mechanistic Implications. J.N. Scarsdale, G. Kazanina, S. Radaev, V. Schirch, and H.T. Wright, Biochemistry 1999, 38, 8347-8358.
A Novel Hydropathic Intermolecular Field Analysis (HIFA) for the Prediction of Ligand-Receptor Binding Affinities. S.F. Semus, Med. Chem. Res. 1999, 9, 535-550.
Discovery of Novel HIV-1 Reverse Transcriptase Inhibitors Using a Combination of 3D Database Searching and 3D QSAR. D.W. Zaharevitz, R. Gussio, A. Wiegand, R. Jalluri, N. Pattabiraman, G.E. Kellogg, L.A. Pallansch, S.S. Yang and R.W. Buckheit, Jr. Med. Chem. Res. 1999, 9, 551-564.
Scoring Peptide(Mimetic)-Protein Interactions. E.E. Moret, M.C. van Wijk, A.S. Kostense and M.B. Gillies, Med. Chem. Res. 1999, 9, 604-620.
Benzoxazoline and Benzimidazoline Derivatives as Novel Aldose Reductase Inhibitors, Part 1: Lead Evolution. K. Nakao, M. Asao, H. Shirai, K. Saito, T. Moriya, M. Matsumoto, Y. Matsuoka and R. Shimuzu, Med. Chem. Res. 1999, 9, 621-630.
Benzoxazoline and Benzimidazoline Derivatives as Novel Aldose Reductase Inhibitors, Part 2: Lead Optimization. K. Nakao, M. Asao, H. Shirai, K. Saito, T. Moriya, M. Matsumoto, Y. Matsuoka and R. Shimuzu, Med. Chem. Res. 1999, 9, 631-642.
Hydropathic Interaction Analysis of Sequence-Specific Heparin Pentasaccharide Binding to Antithrombin. U.R. Desai and G.T. Gunnarsson, Med. Chem. Res. 1999, 9, 643-652.
Interpretation of CoMFA Results - A Probe Set Study Using Hydrophobic Fields. I.K. Pajeva, M. Wiese, Quant. Struct-Act. Relat. 1999, 18, 369-379.
Computational Methodology for Estimating Changes in Free Energes of Biomolecular Associations Upon Mutation. The Importance of Bound Water in Dimer-Tetramer Assembly for 37 Mutant Hemoglobins. J.C. Burnett, G.E. Kellogg and D.J. Abraham, Biochemistry 2000, 39, 1622-1633.
Structure-based Design Modifications of the Paullone Molecular Scaffold for Cyclin-dependent Kinase Inhibition. R. Gussio, D.W. Zaharevitz, C.F. McGrath, N. Pattabiraman, G.E. Kellogg, C. Schultz, A. Link, C. Kunick, M. Loest, L. Meijer and E.A. Sausville, Anti-Cancer Drug Des. 2000, 15, 53-66.
3-D QSAR Analysis of Inhibition of Murine Soluble Epoxide Hydrolase (MsEH) by Benzoylureas, Arylureas, and their Analogues. Y. Nakagawa, C.E. Wheelock, C. Morisseau, M.H. Goodrow, B.G. Hammock and B.D. Hammock, Bioorg. Med. Chem. 2000, 8, 2663-2673.
Application of (Quantitative) Structure-Activity Relationships to Progestagens: from Serendipity to Structure-Based Design. R. Bursi and M.B. Groen, Eur. J. Med. Chem. 2000, 35, 787-796.
Three-Dimensional Quantitative Structure-Activity Relationship Analyses of RGD Mimetics as Fibrinogen Receptor Antagonists. M. Miyashita, M. Akamatsu, Y. Hayashi and T. Ueno, Bioorg. Med. Chem. Lett. 2000, 10, 859-863.
A Comparative Molecular Field Analysis of Inhibitors of Tubulin Polymerization. M. Weigt and M. Wiese, Quant. Struct.-Act. Relat. 2000, 19, 142-148.
HINT Predictive Analysis of Binding between Retinol Binding Protein and Hydrophobic Ligands. A. Marabotti, L. Balestreri, P. Cozzini, A. Mozzarelli, G.E. Kellogg and D.J. Abraham, Bioorg. Med. Chem. Lett. 2000, 10, 2129-2132.
Hydrophobicity: Is LogP_o/w More than the Sum of its Parts? G.E. Kellogg and D.J. Abraham, Eur. J. Med. Chem. 2000, 35, 651-661.
3-D QSAR Analysis of Inhibition of Murine Soluble Epoxide Hydrolase (MsEH) by Benzoylureas, Arylureas, and their Analogues. Y. Nakagawa, C.E. Wheelock, C. Morisseau, M.H. Goodrow, B.G. Hammock and B.D. Hammock, Bioorg. Med. Chem. 2000, 2663-2673.
Computationally Accessible Method for Estimating Free Energy Changes Resulting from Site-Specific Mutations of Biomolecules: Systematic Model Building and Structural/Hydropathic Analysis of Deoxy and Oxy Hemoglobins. J.C. Burnett, P. Botti, D.J. Abraham and G.E. Kellogg, Proteins: Struct. Funct. Genet. 2001, 42, 355-357.
Which Aminoglycoside Ring is Most Important for Binding? A Hydropathic Analysis of Gentamicin, Paromomycin, and Analogues. D.J. Cashman, J.P. Rife and G.E. Kellogg, Biorg. Med. Chem. Lett. 2001, 11, 119-122.
Very Empirical Treatment of Solvation and Entropy: A Force Field Derived from LogP_o/w. G.E. Kellogg, J.C. Burnett and D.J. Abraham, J. Computer-Aided Mol. Design (Persp. Drug Discov. Design) 2001, 15, 381-393.
Progress in Predicting Human ADME Parameters in silico. S. Ekins, C.L. Waller, P.W. Swaan, G. Cruciani, S.A. Wrighton and J.H. Wikel, J. Pharmacol. Toxicol. Meth. 2000, 44, 251-272.
Substructure and Whole Molecule Approaches for Calculating Log P. R. Mannhold and H. van de Waterbeemd, J. Computer-Aided Mol. Design 2001, 15, 337-354.
Structure-Based Design of Inhibitors of the Rice Blast Fungal Enzyme Trihydroxynaphthalene Reductase. D.B. Jordan, G.S. Basarab, D.I. Liao, W.M.P. Johnson, K.N. Winzenberg, and D.A. Winkler, J. Molec. Graph. Modelling 2001, 19, 434.
Molecular Field Analysis of Clozapine Analogs in the Development of a Pharmacophore Model of Antipsychotic Drug Action. B.G. Tehan, E.J. Lloyd and M.G. Wong, J. Molec. Graph. Modelling 2001, 19, 417.
Identification and Characterization of New Inhibitors of the Escherichia Coli MurA Enzyme. E.Z. Baum, D.A. Montenegro, L. Licata, I. Turchi, G.C. Webb, B.D. Foleno and K. Bush, Antimicrobial Agents Chemotherapy 2001, 45, 3182-3188.
QSAR: Hydropathic analysis of inhibitors of the p53-mdm2 interaction. P.S. Galatin and D.J. Abraham, Proteins Str. Funct. Genet. 2001, 45, 169-175.
Designing Small, Nonsugar Activators of Antithrombin Using Hydropathic Interaction Analyses. G.T. Gunnarsson and U.R. Desai, J. Med. Chem. 2002, 45, 1233-1243.
Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 1. Models Without Explicit Constrained Water. P. Cozzini, M. Fornabaio, A. Marabotti, D.J. Abraham, G.E. Kellogg and A. Mozzarelli, J. Med. Chem. 2002, 45, 2469-2483.
Transport and Structural Studies of Sulfonated Styrene-Ethylene Copolymer Membranes. J.M. Serpico, S.G. Ehrenberg, J.J. Fontanella, X. Jiao, D. Perahia, K.A. McGrady, E.H. Sanders, G.E. Kellogg, G.E. Wnek, Macromolecules 2002, 35, 5916-5921.

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