Chemical Computing Group - MOE Citations 2009

2009

Abdel-Megeed, A.M.; Abdel-Rahman, H.M.; Alkaraman, G.-E.S. & El-Gendy, M.A.
Design, Synthesis and Molecular Modeling Study of Acylated 1,2,4-Triazole-3-Acetates with Potential Anti-Inflammatory Activity
European Journal of Medicinal Chemistry 44 (2009) 117–123 doi

Adebiyi, A.P.; Adebiyi, A.O.; Yamashita, J.; Ogawa, T. & Muramoto, K.
Purification and Characterization of Antioxidative Peptides Derived from Rice Bran Protein Hydrolysate
European Food Research and Technology 228 (2009) 553–563 doi

Al-Obaid, A.M.; Abdel-Hamide, S.G.; El-Kashef, H.A.; Abdel-Aziz, A.A.M.; El-Azab, A.S.; Al-Khamees, H.A. & El-Subbagh, H.I.
Substituted quinazolines, part 3. Synthesis, in vitro antitumor activity and molecular modeling study of certain 2-thieno-4(3H)-quinazolinone analogs
European Journal of Medicinal Chemistry 44 (2009) 2379–2391 doi

Appiah-Opong, R.; Commandeur, J.N.M.; Istyastono, E.; Bogaards, J.J. & Vermeulen, N.P.E.
Inhibition of Human Glutathione S-Transferases by Curcumin and Analogues
Xenobiotica 39 (2009) 302–311 doi

Arrault, A.; Rocchi, S.; Picard, F.; Maurois, P.; Pirotte, B. & Vamecq, J.
A Short Series of Antidiabetic Sulfonylureas Exhibit Multiple Ligand PPARγ-binding Patterns
Biomedicine & Pharmacotherapy 63 (2009) 56–62 doi

Ballester, P.J.; Finn, P.W. & Richards, W.G.
Ultrafast Shape Recognition: Evaluating a New Ligand-Based Virtual Screening Technology
Journal of Molecular Graphics and Modelling 27 (2009) 836–845 doi

Barchéchath, S.; Williams, C.I.; Saade, K.; Lauwagie, S. & Jean-Claude, B.
Rational Design of Multitargeted Tyrosine Kinase Inhibitors: A Novel Approach
Chemical Biology & Drug Design 73 (2009) 380–387 doi

Bunch, L.; Gefflaut, T.; Alaux, S.; Sagot, E.; Nielsen, B. & Pickering, D.S.
Pharmacological characterization of (4R)-alkyl glutamate analogues at the ionotropic glutamate receptors—Focus on subtypes iGlu5–7
European Journal of Pharmacology 609 (2009) 1–4 doi

Butler, K.T.; Luque, F.J. & Barril, X.
Toward Accurate Relative Energy Predictions of the Bioactive Conformation of Drugs
Journal of Computational Chemistry 30 (2009) 601–610 doi

Carrascal, N. & Rizzo, R.C.
Calculation of Binding Free Energies for Non-Zinc Chelating Pyrimidine Dicarboxamide Inhibitors with MMP-13
Bioorganic & Medicinal Chemistry Letters 19 (2009) 47–50 doi

Catana, C.
Simple Idea to Generate Fragment and Pharmacophore Descriptors and Their Implications in Chemical Informatics
Journal of Chemical Information and Modeling 49 (2009) 543–548 doi

Cee, V.J.; Cheng, A.C.; Romero, K.; Bellon, S.; Mohr, C.; Whittington, D.A.; Bak, A.; Bready, J.; Caenepeel, S.; Coxon, A.; Deak, H.L.; Fretland, J.; Gu, Y.; Hodous, B.L.; Huang, X.; Kim, J.L.; Lin, J.; Long, A.M.; Nguyen, H.; Olivieri, P.R.; Patel, V.F.; Wang, L.; Zhoud, Y.; Hughes, P. & Geuns-Meyer, S.
Pyridyl-pyrimidine Benzimidazole Derivatives as Potent, Selective, and Orally Bioavailable Inhibitors of Tie-2 Kinase
Bioorganic & Medicinal Chemistry Letters 19 (2009) 424–427 doi

Chegaev, K.; Cena, C.; Giorgis, M.; Rolando, B.; Tosco, P.; Bertinaria, M.; Fruttero, R.; Carrupt, P.-A. & Gasco, A.
Edaravone Derivatives Containing NO-Donor Functions
Journal of Medicinal Chemistry 52 (2009) 574–578 doi

Chen, Z.; Wen, F.; Sun, N. & Zhao, H.
Directed Evolution of Homing Endonuclease I-SceI with Altered Sequence Specificity
Protein Engineering, Design and Selection 22 (2009) 249–256 doi

Cichero, E.; Casolino, C.; Menozzi, G.; Mosti, L. & Fossa, P.
Exploring the QSAR of Pyrazolo [3,4-b] Pyridine, Pyrazolo [3,4-b] Pyridone and Pyrazolo [3,4-b] Pyrimidine Derivatives as Antagonists for A₁ Adenosine Receptor
QSAR & Combinatorial Science 28 (2009) 426–435 doi

Cichero, E.; Cesarini, S.; Fossa, P.; Spallarossa, A. & Mosti, L.
Thiocarbamates as non-nucleoside HIV-1 reverse transcriptase inhibitors: Docking-based CoMFA and CoMSIA analyses
European Journal of Medicinal Chemistry 44 (2009) 2059–2070 doi

Clark, A.M. & Labute, P.
Detection and Assignment of Common Scaffolds in Project Databases of Lead Molecules
Journal of Medicinal Chemistry 52 (2009) 469–483 doi

Colotta, V.; Lenzi, O.; Catarzi, D.; Varano, F.; Filacchioni, G.; Martini, C.; Trincavelli, L.; Ciampi, O.; Pugliese, A.M.; Traini, C.; Pedata, F.; Morizzo, E. & Moro, S.
Pyrido[2,3-e]-1,2,4-triazolo[4,3-a]pyrazin-1-one as a New Scaffold To Develop Potent and Selective Human A₃ Adenosine Receptor Antagonists. Synthesis, Pharmacological Evaluation, and Ligand–Receptor Modeling Studies
Journal of Medicinal Chemistry 52 (2009) 2407–2419 doi

Cummings, C.G.; Ross, N.T.; Katt, W.P. & Hamilton, A.D.
Synthesis and Biological Evaluation of a 5-6-5 Imidazole-Phenyl-Thiazole Based α-Helix Mimetic
Organic Letters 11 (2009) 25–28 doi

Deeth, R.J.; Anastasi, A.; Diedrich, C. & Randell, K.
Molecular Modelling for Transition Metal Complexes: Dealing with d-Electron Effects
Coordination Chemistry Reviews 253 (2009) 795–816 doi

Delp, S.A.; Munro-Leighton, C.; Khosla, C.; Templeton, J.L.; Alsop, N.M.; Gunnoe, T.B. & Cundari, T.R.
Combined Experimental and Computational Study of W(II), Ru(II), Pt(IV) and Cu(I) Amine and Amido Complexes Using ¹⁵N NMR Spectroscopy
Journal of Organometallic Chemistry 694 (2009) 1549–1556 doi

den Hollander, A.; McGee, T.L.; Ziviello, C.; Banfi, S.; Dryja, T.P.; Gonzalez-Fernandez, F.; Ghosh, D. & Berson, E.
A Homozygous Missense Mutation in the IRBP Gene (RBP3) Associated with Autosomal Recessive Retinitis Pigmentosa
Investigative Ophthalmology & Visual Science 50 (2009) 1864–1872 doi

Deshpande, S.; Solomon, V.R.; Katti, S.B. & Prabhakar, Y.
Topological Descriptors in Modelling Antimalarial Activity: N¹-(7-chloro-4-quinolyl)-1,4-bis (3-aminopropyl) Piperazine as Prototype
Journal of Enzyme Inhibition and Medicinal Chemistry 24 (2009) 94–104 doi

Elsässer, B.; Valiev, M. & Weare, J.H.
A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction
Journal of the American Chemical Society 131 (2009) 3869–3871 doi

Enomoto, H.; Morikawa, Y.; Miyake, Y.; Tsuji, F.; Mizuchi, M.; Suhara, H.; Fujimura, K.; Horiuchi, M. & Ban, M.
Synthesis and Biological Evaluation of N-Mercaptoacylcysteine Derivatives as Leukotriene A₄ Hydrolase Inhibitors
Bioorganic & Medicinal Chemistry Letters 19 (2009) 442–446 doi

Ermondi, G.; Cravotto, G. & Balliano, G.
Umbelliferone aminoalkyl derivatives as inhibitors of human oxidosqualene-lanosterol cyclase
Journal of Enzyme Inhibition and Medicinal Chemistry 24 (2009) 589–598 doi

Erős, D.; Őrfi, L.; Csuka, I.; Kéri, G. & Hrabák, A.
Binding Specificity of the L-Arginine Transport Systems in Mouse Macrophages and Human Cells Overexpressing the Cationic Amino Acid Transporter hCAT-1
Amino Acids 36 (2009) 483–492 doi

Fjell, C.D.; Jenssen, H.; Hilpert, K.; Cheung, W.A.; Panté, N.; Hancock, R.E.W. & Cherkasov, A.
Identification of Novel Antibacterial Peptides by Chemoinformatics and Machine Learning
Journal of Medicinal Chemistry 52 (2009) 2006–2015 doi

Francalanci, F.; Avolio, M.; De Luca, E.; Longo, D.; Menchise, V.; Guazzi, P.; Sgrň, F.; Marino, M.; Goitre, L.; Balzac, F.; Trabalzini, L. & Retta, S.F.
Structural and Functional Differences between KRIT1A and KRIT1B Isoforms: A Framework for Understanding CCM Pathogenesis
Experimental Cell Research 315 (2009) 285–303 doi

Ghosh, D.; Griswold, J.; Erman, M. & Pangborn, W.
Structural Basis for Androgen Specificity and Oestrogen Synthesis in Human Aromatase
Nature 457 (2009) 219–223 doi

Gleeson, M.P. & Gleeson, D.
QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?
Journal of Chemical Information and Modeling 49 (2009) 670–677 doi

Gooptu, B.; Miranda, E.; Nobeli, I.; Mallya, M.; Purkiss, A.; Leigh Brown, S.C.; Summers, C.; Phillips, R.L.; Lomas, D.A. & Barrett, T.E.
Crystallographic and Cellular Characterisation of Two Mechanisms Stabilising the Native Fold of α1-Antitrypsin: Implications for Disease and Drug Design
Journal of Molecular Biology 387 (2009) 857–868 doi

Green, R.C.E.; Thumser, A.E.; Povey, D.; Saldanha, J.W.; Potter, B.S.; Palmer, R.A. & Howlin, B.J.
A Comparative Study of the Single Crystal X-ray Determination and Molecular Modelling of the Binding of Oligomycin to ATP Synthase
Computational Biology and Chemistry (2009) doi

Grycova, L.; Sklenovsky, P.; Lansky, Z.; Janovska, M.; Otyepka, M.; Amler, E.; Teisinger, J. & Kubala, M.
ATP and magnesium drive conformational changes of the Na⁺/K^--ATPase cytoplasmic headpiece
Biochimica et Biophysica Acta - Biomembranes 1788 (2009) 1081–1091 doi

Guo, H.; Gorin, A. & Guo, H.
A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel β-Sheets
Interdisciplinary Sciences: Computational Life Sciences 1 (2009) 12–20 doi

Hähnke, V.; Hofmann, B.; Grgat, T.; Proschak, E.; Steinhilber, D. & Schneider, G.
PhAST: Pharmacophore Alignment Search Tool
Journal of Computational Chemistry 30 (2009) 761–771 doi

Harada, M.; Murakami, H.; Okawa, A.; Okimoto, N.; Hiraoka, S.; Nakahara, T.; Akasaka, R.; Shiraishi, Y.; Futatsugi, N.; Mizutani-Koseki, Y.; Kuroiwa, A.; Shirouzu, M.; Yokoyama, S.; Taiji, M.; Iseki, S.; Ornitz, D.M. & Koseki, H.
FGF9 Monomer–Dimer Equilibrium Regulates Extracellular Matrix Affinity and Tissue Diffusion
Nature Genetics 41 (2009) 289–298 doi

Hecht, D. & Fogel, G.B.
A Novel In Silico Approach to Drug Discovery via Computational Intelligence
Journal of Chemical Information and Modeling 49 (2009) 1105–1121 doi

Heinke, R.; Spannhoff, A.; Meier, R.; Trojer, P.; Bauer, I.; Jung, M. & Sippl, W.
Virtual Screening and Biological Characterization of Novel Histone Arginine Methyltransferase PRMT1 Inhibitors
ChemMedChem 4 (2009) 69–77 doi

Hödl, C.; Raunegger, K.; Strommer, R.; Ecker, G.F.; Kunert, O.; Sturm, S.; Seger, C.; Haslinger, E.; Steiner, R.; Strauss, W.S.L. & Schramm, H.-W.
Syntheses and Antigestagenic Activity of Mifepristone Derivatives
Journal of Medicinal Chemistry 52 (2009) 1268–1274 doi

Huang, Y.-m. & Bystroff, C.
Complementation and Reconstitution of Fluorescence from Circularly Permuted and Truncated Green Fluorescent Protein
Biochemistry 48 (2009) 929–940 doi

Imai, Y.N.; Ryu, S. & Oiki, S.
Docking Model of Drug Binding to the Human Ether-à-go-go Potassium Channel Guided by Tandem Dimer Mutant Patch-Clamp Data: A Synergic Approach
Journal of Medicinal Chemistry 52 (2009) 1630–1638 doi

Islam, K.M.D.; Dilcher, M.; Thurow, C.; Vock, C.; Krimmelbein, I.K.; Tietze, L.F.; Gonzalez, V.; Zhao, H. & Gatz, C.
Directed Evolution of Estrogen Receptor Proteins with Altered Ligand-binding Specificities
Protein Engineering, Design and Selection 22 (2009) 45–52 doi

Jackson, T.A.; Robertson, V.; Imberty, A. & Auzanneau, F.I.
The flexibility of the LeaLex Tumor Associated Antigen central fragment studied by systematic and stochastic searches as well as dynamic simulations
Bioorganic & Medicinal Chemistry 17 (2009) 1514–1526 doi

Johnson, S.M.; Connelly, S.; Wilson, I.A. & Kelly, J.W.
Toward Optimization of the Second Aryl Substructure Common to Transthyretin Amyloidogenesis Inhibitors Using Biochemical and Structural Studies
Journal of Medicinal Chemistry 52 (2009) 1115–1125 doi

Kato-Takagaki, K.; Mizukoshi, Y.; Yoshizawa, Y.; Akazawa, D.; Torii, Y.; Ono, K.; Tanimura, R.; Shimada, I. & Takahashi, H.
Structural and Interaction Analysis of Glycoprotein VI-binding Peptide Selected from Phage Display Library
Journal of Biological Chemistry 284 (2009) 10720–10727 doi

Kawashima, T.; Bao, Y.C.; Minoshima, Y.; Nomura, Y.; Hatori, T.; Hori, T.; Fukagawa, T.; Fukada, T.; Takahashi, N.; Nosaka, T.; Inoue, M.; Sato, T.; Kukimoto-Niino, M.; Shirouzu, M.; Yokoyama, S. & Kitamura, T.
A Rac GTPase activating protein MgcRacGAP is an NLS-containing nuclear chaperone in the activation of STAT transcription factors
Molecular and Cellular Biology 29 (2009) 1796–1813 doi

Koba, H.; Okuda, K.; Watanabe, H.; Tagami, J. & Senpuku, H.
Role of lysine in interaction between surface protein peptides of Streptococcus gordonii and agglutinin peptide
Oral Microbiology and Immunology 24 (2009) 162–169 doi

Koeberle, A.; Siemoneit, U.; Northoff, H.; Hofmann, B.; Schneider, G. & Werz, O.
MK-886, an inhibitor of the 5-lipoxygenase-activating protein, inhibits cyclooxygenase-1 activity and suppresses platelet aggregation
European Journal of Pharmacology 608 (2009) 804–890 doi

Kortagere, S.; Krasowski, M.D. & Ekins, S.
The importance of discerning shape in molecular pharmacology
Trends in Pharmacological Sciences 30 (2009) 138–147 doi

Krasowski, M.D.; Siam, M.G.; Iyer, M.; Pizon, A.F.; Giannoutsos, S. & Ekins, S.
Chemoinformatic Methods for Predicting Interference in Drug of Abuse/Toxicology Immnoassays
Clinical Chemistry (2009) doi

Kularatne, S.A.; Zhou, Z.; Yang, J.; Post, C.B. & Low, P.S.
Design, Synthesis, and Pre-clinical Evaluation of Prostate-Specific Membrane Antigen (PSMA)-Targeted 99mTc-Radioimaging Agents
Molecular Pharmaceutics (2009) doi

La Motta, C.; Sartini, S.; Mugnaini, L.; Salerno, S.; Simorini, F.; Taliani, S.; Marini, A.M.; Da Settimo, F.; Lavecchia, A.; Novellino, E.; Antonioli, L.; Fornai, M.; Blandizzi, C. & Del Tacca, M.
Exploiting the Pyrazolo[3,4-d]pyrimidin-4-one Ring System as a Useful Template To Obtain Potent Adenosine Deaminase Inhibitors
Journal of Medicinal Chemistry 52 (2009) 1681–1692 doi

Lambertucci, C.; Antonini, I.; Buccioni, M.; Ben, D.D.; Kachare, D.D.; Volpini, R.; Klotz, K.-N. & Cristalli, G.
8-Bromo-9-alkyl adenine derivatives as tools for developing new adenosine A_2A and A_2B receptors ligands
Bioorganic & Medicinal Chemistry 17 (2009) 2812–2822 doi

Lebsack, A.D.; Branstetter, B.J.; Hack, M.D.; Xiao, W.; Peterson, M.L.; Nasser, N.; Maher, M.P.; Ao, H.; Bhattacharya, A.; Kansagara, M.; Scott, B.P.; Luo, L.; Rynberg, R.; Rizzolio, M.; Chaplana, S.R.; Wickenden, A.D. & Breitenbucher, J.G.
Identification and Synthesis of 2,7-diamino-thiazolo [5,4-d] Pyrimidine Derivatives as TRPV1 Antagonists
Bioorganic & Medicinal Chemistry Letters 19 (2009) 40–46 doi

Lehto, P.; Aaltonen, J.; Tenho, M.; Rantanen, J.; Hirvonen, J.; Tanninen, V.P. & Peltonen, L.
Solvent-Mediated Solid Phase Transformations of Carbamazepine: Effects of Simulated Intestinal Fluid and Fasted State Simulated Intestinal Fluid
Journal of Pharmaceutical Sciences 98 (2009) 985–996 doi

Lin, Y.S.; Yasuda, K.; Assem, M.; Cline, C.; Barber, J.; Li, C.-W.; Kholodovych, V.; Ai, N.; Chen, J.D.; Welsh, W.J.; Sean Ekins & Schuetz, E.G.
The Major Human PXR Splice Variant, PXR.2, Exhibits Significantly Diminished Ligand-activated Transcriptional Regulation
Drug Metabolism and Disposition (2009) doi

Lounkine, E. & Bajorath, J.
Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds
Journal of Chemical Information and Modeling 49 (2009) 162–168 doi

Maeda, M.H. & Kinoshita, K.
Development of New Indices to Evaluate Protein-Protein Interfaces: Assembling Space Volume, Assembling Space Distance, and Global Shape Descriptor
Journal of Molecular Graphics and Modelling 27 (2009) 706–711 doi

Markt, P.; Feldmann, C.; Rollinger, J.M.; Raduner, S.; Schuster, D.; Kirchmair, J.; Distinto, S.; Spitzer, G.M.; Wolber, G.; Laggner, C.; Altmann, K.-H.; Langer, T. & Gertsch, J.
Discovery of Novel CB₂ Receptor Ligands by a Pharmacophore-Based Virtual Screening Workflow
Journal of Medicinal Chemistry 52 (2009) 369–378 doi

Marx, I.E.; DiMauro, E.F.; Cheng, A.; Emkey, R.; Hitchcock, S.A.; Huang, L.; Huang, M.Y.; Human, J.; Lee, J.H.; Li, X.; Martin, M.W.; White, R.D.; Fremeau Jr., R.T. & Patel, V.F.
Discovery of α-amidosulfones as Potent and Selective Agonists of CB₂: Synthesis, SAR, and Pharmacokinetic Properties
Bioorganic & Medicinal Chemistry Letters 19 (2009) 31–35 doi

Masciocchi, J.; Frau, G.; Fanton, M.; Sturlese, M.; Floris, M.; Pireddu, L.; Palla, P.; Cedrati, F.; Rodriguez-Tomé, P. & Moro, S.
MMsINC: A Large-scale Chemoinformatics Database
Nucleic Acids Research 37 (2009) D284–D290 doi

Matthews, L.; Berry, A.; Tersigni, M.; D'Acquisto, F.; Ianaro, A. & Ray, D.
Thiazolidinediones Are Partial Agonists for the Glucocorticoid Receptor
Endocrinology 150 (2009) 75–86 doi

McGuigan, C.; Bidet, O.; Derudas, M.; Andrei, G.; Snoeck, R. & Balzarini, J.
Alkenyl substituted bicyclic nucleoside analogues retain nanomolar potency against Varicella Zoster Virus
Bioorganic & Medicinal Chemistry 17 (2009) 3025–3027 doi

Medina-Franco, J.L.; Martínez-Mayorga, K.; Bender, A.; Marín, R.M.; Giulianotti, M.A.; Pinilla, C. & Houghten, R.A.
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs
Journal of Chemical Information and Modeling 49 (2009) 477–491 doi

Miao, L. & Schulten, K.
Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics
Structure 17 (2009) 449–459 doi

Miller, J.R.; Dunham, S.; Mochalkin, I.; Banotai, C.; Bowman, M.; Buist, S.; Dunkle, B.; Hanna, D.; Harwood, H.J.; Huband, M.D.; Karnovsky, A.; Kuhn, M.; Limberakis, C.; Liu, J.Y.; Mehrens, S.; Mueller, W.T.; Narasimhan, L.; Ogden, A.; Ohren, J.; Prasad, J.V.N.V.; Shelly, J.A.; Skerlos, L.; Sulavik, M.; Thomas, V.H.; VanderRoest, S.; Wang, L.; Wang, Z.; Whitton, A.; Zhu, T. & Stover, C.K.
A Class of Selective Antibacterials Derived From a Protein Kinase Inhibitor Pharmacophore
Proceedings of the National Academy of Sciences U.S.A. 106 (2009) 1737–1742 doi

Mitchell, W.L.; Giblin, G.M.P.; Naylor, A.; Eatherton, A.J.; Slingsby, B.P.; Rawlings, A.D.; Jandu, K.S.; Haslam, C.P.; Brown, A.J.; Goldsmith, P.; Clayton, N.M.; Wilson, A.W.; Chessell, I.P.; Green, R.H.; Whittington, A.R. & Wall, I.D.
Pyridine-3-carboxamides as Novel CB₂ Agonists for Analgesia
Bioorganic & Medicinal Chemistry Letters 19 (2009) 259–263 doi

Miyamoto, S.; Kawai, A.; Higuchi, S.; Nishi, Y.; Tanimoto, T.; Uekaji, Y.; Nakata, D.; Fukumi, H. & Terao, K.
Structural Studies of Coenzyme Q10 Inclusion Complex with γ-cyclodextrin Using Chemical Analyses and Molecular Modeling
Chem-Bio Informatics Journal 9 (2009) 1–11 doi

Mulakala, C. & Kaznessis, Y.N.
Path-Integral Method for Predicting Relative Binding Affinities of Protein–Ligand Complexes
Journal of the American Chemical Society 131 (2009) 4521–4528 doi

Neres, J.; Brewer, M.L.; Ratier, L.; Botti, H.; Buschiazzo, A.; Edwards, P.N.; Mortenson, P.N.; Charlton, M.H.; Alzari, P.M.; Frasch, A.C.; Bryce, R.A. & Douglas, K.T.
Discovery of Novel Inhibitors of Trypanosoma cruzi trans-sialidase from in silico Screening
Bioorganic & Medicinal Chemistry Letters 19 (2009) 589–596 doi

Niimi, N.; Sassa, A.; Katafuchi, A.; Grúz, P.; Fujimoto, H.; Bonala, R.-R.; Johnson, F.; Ohta, T. & Nohmi, T.
The Steric Gate Amino Acid Tyrosine 112 Is Required for Efficient Mismatched-Primer Extension by Human DNA Polymerase κ
Biochemistry (2009) doi

Okada, Y.; Murayama, N.; Yanagida, C.; Shimizu, M.; Guengerich, F.P. & Yamazaki, H.
Drug Interactions of Thalidomide with Midazolam and Cyclosporine A: Heterotropic Cooperativity of Human Cytochrome P450 3A5
Drug Metabolism and Disposition 37 (2009) 18–23 doi

Okano, M.; Mito, J.; Maruyama, Y.; Masuda, H.; Niwa, T.; Nakagawa, S.; Nakamura, Y. & Matsuura, A.
Discovery and structure-activity relationships of 4-aminoquinazoline derivatives, a novel class of opioid receptor like-1 (ORL1) antagonists
Bioorganic & Medicinal Chemistry 17 (2009) 119–132 doi

Okazaki, S.; Suzuki, A.; Mizushima, T.; Kawano, T.; Komeda, H.; Asano, Y. & Yamane, T.
The Novel Structure of a Pyridoxal 5′-Phosphate-Dependent Fold-Type I Racemase, α-Amino-ε-caprolactam Racemase from Achromobacter obae
Biochemistry 48 (2009) 941–950 doi

Oyarzabal, J.; Howe, T.; Alcazar, J.; Andrés, J.I.; Alvarez, R.M.; Dautzenberg, F.; Iturrino, L.; Martínez, S. & Van der Linden, I.
Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and a Prospective Case Study: New Melanin Concentrating Hormone Antagonists
Journal of Medicinal Chemistry 52 (2009) 2076–2089 doi

Ozaki, M. & Seto, T.
Noble Gas Anesthetics and Immobilizers Show Different Binding Distributions to KcsA Channel
Biophysical Journal 96 (2009) 40a doi

Pabuwal, V. & Li, Z.
Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins
Protein Engineering, Design and Selection 22 (2009) 67–73 doi

Pautus, S.; Aboraia, A.S.; Bassett, C.E.; Brancale, A.; Coogan, M.P. & Simons, C.
Design and synthesis of substituted imidazole and triazole N-phenylbenzo [d] oxazolamine inhibitors of retinoic acid metabolizing enzyme CYP26
Journal of Enzyme Inhibition and Medicinal Chemistry 24 (2009) 487–498 doi

Peach, M.L.; Tan, N.; Choyke, S.J.; Giubellino, A.; Athauda, G.; Burke, T.R.; Nicklaus, M.C. & Bottaro, D.P.
Directed Discovery of Agents Targeting the Met Tyrosine Kinase Domain by Virtual Screening
Journal of Medicinal Chemistry 52 (2009) 943–951 doi

Pedras, B.; Oliveira, E.; Santos, H.; Rodríguez, L.; Crehuet, R.; Avilés, T.; Capelo, J.L. & Lodeiro, C.
A new tripodal poly-imine indole-containing ligand: Synthesis, complexation, spectroscopic and theoretical studies
Inorganica Chimica Acta 362 (2009) 2627–2635 doi

Pellegrino, S.; Clerici, F.; Contini, A.; Leone, S.; Pilati, T. & Gelmi, M.L.
Chemoselective asymmetric synthesis of C-3a-(3-hydroxypropyl)-tetrahydropyrrolo[2,3-b]indole and C-4a-(2-aminoethyl)-tetrahydropyrano[2,3-b]indole derivatives
Tetrahedron 65 (2009) 1995–2004 doi

Pérez-Nueno, V.I.; Pettersson, S.; Ritchie, D.W.; Borrell, J.I. & Teixidó, J.
Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening
Journal of Chemical Information and Modeling 49 (2009) 810–823 doi

Pérez-Nueno, V.I.; Rabal, O.; Borrell, J.I. & Teixidó, J.
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
Journal of Chemical Information and Modeling (2009) doi

Pérez-Toledo, K.; Rojas-Meza, A.P.; Mancio-Silva, L.; Hernández-Cuevas, N.A.; Delgadillo, D.M.; Vargas, M.; Martínez-Calvillo, S.; Scherf, A. & Hernandez-Rivas, R.
Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes
Nucleic Acids Research (2009) doi

Piscitelli, F.; Coluccia, A.; Brancale, A.; La Regina, G.; Sansone, A.; Giordano, C.; Balzarini, J.; Maga, G.; Zanoli, S.; Samuele, A.; Cirilli, R.; La Torre, F.; Lavecchia, A.; Novellino, E. & Silvestri, R.
Indolylarylsulfones Bearing Natural and Unnatural Amino Acids. Discovery of Potent Inhibitors of HIV-1 Non-Nucleoside Wild Type and Resistant Mutant Strains Reverse Transcriptase and Coxsackie B4 Virus
Journal of Medicinal Chemistry 52 (2009) 1922–1934 doi

Rupp, M.; Schneider, P. & Schneider, G.
Distance Phenomena in High-Dimensional Chemical Descriptor Spaces: Consequences for Similarity-Based Approaches
Journal of Computational Chemistry (2009) doi

Sabbaghian, M.; Ebrahim-Habibi, A. & Nemat-Gorgani, M.
Thermal aggregation of a model allosteric protein in different conformational states
International Journal of Biological Macromolecules 44 (2009) 156–162 doi

Sapino, S.; Carlotti, M.; Caron, G.; Ugazio, E. & Cavalli, R.
In silico design, photostability and biological properties of the complex resveratrol/hydroxypropyl-β-cyclodextrin
Journal of Inclusion Phenomena and Macrocyclic Chemistry 63 (2009) 171–180 doi

Shadnia, H.; Wright, J.S. & Anderson, J.M.
Interaction Force Diagrams: New Insight into Ligand-Receptor Binding
Journal of Computer-Aided Molecular Design 23 (2009) 185–194 doi

Shakesby, A.J.; Wallace, I.S.; Isaacs, H.V.; Pritchard, J.; Roberts, D.M. & Douglas, A.E.
A water-specific aquaporin involved in aphid osmoregulation
Insect Biochemistry and Molecular Biology 1 (2009) 1–10 doi

Singh, N.; Guha, R.; Giulianotti, M.A.; Pinilla, C.; Houghten, R.A. & Medina-Franco, J.L.
Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository
Journal of Chemical Information and Modeling 49 (2009) 1010–1024 doi

Spies, M.A.; Reese, J.G.; Dodd, D.; Pankow, K.L.; Blanke, S.R. & Baudry, J.
Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase
Journal of the American Chemical Society 131 (2009) 5274–5284 doi

Suenaga, A.; Hatakeyama, M.; Kiyatkin, A.; Radhakrishnan, R.; Taiji, M. & Kholodenko, B.
Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor
Biophysical Journal 96 (2009) 2278–2288 doi

Tagami, A.; Ishibashi, N.; Kato, D.; Taguchi, N.; Mochizuki, Y.; Watanabe, H.; Ito, M. & Tanaka, S.
Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method
Chemical Physics Letters 472 (2009) 118–123 doi

Taguchi, N.; Mochizuki, Y.; Nakano, T.; Amari, S.; Fukuzawa, K.; Ishikawa, T.; Sakurai, M. & Tanaka, S.
Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)
The Journal of Physical Chemistry B 113 (2009) 1153–1161 doi

Thiry, A.; Ledecq, M.; Cecchi, A.; Frederick, R.; Dogné, J.M.; Supuran, C.T.; Wouters, J. & Masereel, B.
Ligand-based and structure-based virtual screening to identify carbonic anhydrase IX inhibitors
Bioorganic & Medicinal Chemistry 17 (2009) 553–557 doi

Thorsteinson, N.; Ban, F.; Santos-Filho, O.; Tabaei, S.M.H.; Miguel-Queralt, S.; Underhill, C.; Cherkasov, A. & Hammond, G.L.
In Silico Identification of Anthropogenic Chemicals As Ligands of Zebrafish Sex Hormone Binding Globulin
Toxicology and Applied Pharmacology 234 (2009) 47–57 doi

Topiol, S. & Sabio, M.
X-ray structure breakthroughs in the GPCR transmembrane region
Biochemical Pharmacology (2009) doi

Tosco, P.; Ahring, P.K.; Dyhring, T.; Peters, D.; Harpsøe, K.; Liljefors, T. & Balle, T.
Complementary Three-Dimensional Quantitative Structure–Activity Relationship Modeling of Binding Affinity and Functional Potency: A Study on α₄β₂ Nicotinic Ligands
Journal of Medicinal Chemistry 52 (2009) 2311–2316 doi

Tran, T.D.; Park, H.; Kim, H.P.; Ecker, G.F. & Thai, K.M.
Inhibitory activity of prostaglandin E2 production by the synthetic 2'-hydroxychalcone analogues: Synthesis and SAR study
Bioorganic & Medicinal Chemistry Letters 19 (2009) 1650–1653 doi

Tresadern, G.; Bemporad, D. & Howe, T.
A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor
Journal of Molecular Graphics and Modelling (2009) doi

Ulens, C.; Akdemir, A.; Jongejan, A.; van Elk, R.; Bertrand, S.; Perrakis, A.; Leurs, R.; Smit, A.B.; Sixma, T.K.; Bertrand, D. & de Esch, I.J.P.
Use of Acetylcholine Binding Protein in the Search for Novel α7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X-ray Analysis
Journal of Medicinal Chemistry 52 (2009) 2372–2383 doi

Vanlaer, S.; Voet, A.; Gielens, C.; De Maeyer, M. & Compernolle, F.
Bridged 5,6,7,8-Tetrahydro-1,6-naphthyridines, Analogues of Huperzine A: Synthesis, Modelling Studies and Evaluation as Inhibitors of Acetylcholinesterase
European Journal of Organic Chemistry 5 (2009) 643–654 doi

Vasanthanathan, P.; Hritz, J.; Taboureau, O.; Olsen, L.; Jørgensen, F.S.; Vermeulen, N.P.E. & Oostenbrink, C.
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands
Journal of Chemical Information and Modeling 49 (2009) 43–52 doi

Vasanthanathan, P.; Taboureau, O.; Oostenbrink, C.; Vermeulen, N.P.E.; Olsen, L. & Jørgensen, F.S.
Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques
Drug Metabolism and Disposition 37 (2009) 658–664 doi

Wassermann, A.M.; Geppert, H. & Bajorath, J.
Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors
Journal of Chemical Information and Modeling 49 (2009) 582–592 doi

Watanabe, H.; Matsumaru, H.; Ooishi, A.; Feng, Y.; Odahara, T.; Suto, K. & Honda, S.
Optimizing pH-response of affinity between protein G and IgG Fc: How electrostatic modulations affect protein-protein interactions
Journal of Biological Chemistry 284 (2009) 12373–12383 doi

Watanabe, T.; Arisawa, M.; Narusuye, K.; Alam, M.S.; Yamamoto, K.; Mitomi, M.; Ozoe, Y. & Nishida, A.
Alantrypinone and its derivatives: Synthesis and antagonist activity toward insect GABA receptors
Bioorganic & Medicinal Chemistry 17 (2009) 94–110 doi

Wawer, M.; Peltason, L. & Bajorath, J.
Elucidation of Structure—Activity Relationship Pathways in Biological Screening Data
Journal of Medicinal Chemistry 52 (2009) 1075–1080 doi

Weill, N. & Rognan, D.
Development and Validation of a Novel Protein–Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands
Journal of Chemical Information and Modeling 49 (2009) 1049–1062 doi

Wichapong, K.; Lindner, M.; Pianwanit, S.; Kokpol, S. & Sippl, W.
Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors
European Journal of Medicinal Chemistry 44 (2009) 1383–1395 doi

Williamson, D.S.; Borgognoni, J.; Clay, A.; Daniels, Z.; Dokurno, P.; Drysdale, M.J.; Foloppe, N.; Francis, G.L.; Graham, C.J.; Howes, R.; Macias, A.T.; Murray, J.B.; Parsons, R.; Shaw, T.; Surgenor, A.E.; Terry, L.; Wang, Y.; Wood, M. & Massey, A.J.
Novel Adenosine-Derived Inhibitors of 70 kDa Heat Shock Protein, Discovered Through Structure-Based Design
Journal of Medicinal Chemistry 52 (2009) 1510–1513 doi

Zhang, Y.; Cao, R.; Yin, F.; Hudock, M.P.; Guo, R.-T.; Krysiak, K.; Mukherjee, S.; Gao, Y.-G.; Robinson, H.; Song, Y.; No, J.H.; Bergan, K.; Leon, A.; Cass, L.; Goddard, A.; Chang, T.-K.; Lin, F.-Y.; Van Beek, E.; Papapoulos, S.; Wang, A.H.-J.; Kubo, T.; Ochi, M.; Mukkamala, D. & Oldfield, E.
Lipophilic Bisphosphonates as Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-ray and NMR Investigation
Journal of the American Chemical Society 131 (2009) 5153–5162 doi