Journal of Computer-Aided Molecular Design, Volume 23

Volume 23, Number 1, January 2009

• Ling Kang, Honglin Li, Hualiang Jiang, Xicheng Wang:
  An improved adaptive genetic algorithm for protein-ligand docking. 1-12
  
• Li Xing, Ravi G. Kurumbail, Ronald B. Frazier, Michael S. Davies, Hideji Fujiwara, Robin A. Weinberg, James K. Gierse, Nicole Caspers, Jeffrey S. Carter, Joseph J. McDonald, William M. Moore, Michael L. Vazquez:
  Homo-timeric structural model of human microsomal prostaglandin E synthase-1 and characterization of its substrate/inhibitor binding interactions. 13-24
  
• Kirandeep Kaur, Tanaji T. Talele:
  Structure-based CoMFA and CoMSIA study of indolinone inhibitors of PDK1. 25-36
  
• Jufang Shan, Jie J. Zheng:
  Optimizing Dvl PDZ domain inhibitor by exploring chemical space. 37-47
  
• William Novak, Hongming Wang, Goran Krilov:
  Role of protein flexibility in the design of Bcl-X_L targeting agents: insight from molecular dynamics. 49-61
  

Volume 23, Number 2, February 2009

• Jacob Kongsted, Ulf Ryde:
  An improved method to predict the entropy term with the MM/PBSA approach. 63-71
  
• Susanne Eyrisch, Volkhard Helms:
  What induces pocket openings on protein surface patches involved in protein-protein interactions? 73-86
  
• Sage Arbor, Garland R. Marshall:
  A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. 87-95
  
• Mark L. Lewis, Lourdes Cucurull-Sanchez:
  Structural pairwise comparisons of HLM stability of phenyl derivatives: Introduction of the Pfizer metabolism index (PMI) and metabolism-lipophilicity efficiency (MLE). 97-103
  
• Mohamed Zerara, Jürgen Brickmann, Robert Kretschmer, Thomas E. Exner:
  Parameterization of an empirical model for the prediction of n -octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients. 105-111
  
• Sivaprakasam Prasanna, Pankaj R. Daga, Aihua Xie, Robert J. Doerksen:
  Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking. 113-127
  

Volume 23, Number 3, March 2009

• Peng Zhou, Xiang Chen, Zhicai Shang:
  Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities. 129-141
  
• Giovanni Cincilla, David Vidal, Miquel Pons:
  An improved scoring function for suboptimal polar ligand complexes. 143-152
  
• Hongwei Zhou, Wai-Ping Lai, Zhiqiang Zhang, Wai-Kee Li, Hon-Yeung Cheung:
  Computational study on the molecular inclusion of andrographolide by cyclodextrin. 153-162
  
• Yoshito Sawada, Shinya Honda:
  ProSeg: a database of local structures of protein segments. 163-169
  
• Rubén Gil-Redondo, Jorge Estrada, Antonio Morreale, Fernando Herranz, Javier Sancho, Angel R. Ortiz:
  VSDMIP: virtual screening data management on an integrated platform. 171-184
  
• Hooman Shadnia, James S. Wright, James M. Anderson:
  Interaction force diagrams: new insight into ligand-receptor binding. 185-194
  

Volume 23, Number 4, April 2009

• Wendy A. Warr:
  ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). 195-198
  
• Salih Jabour, Mazen Y. Hamed:
  Binding of the Zn²⁺ ion to ferric uptake regulation protein from E. coli and the competition with Fe²⁺ binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur. 199-208
  
• Md. Afroz Alam, Pradeep Kumar Naik:
  Molecular modelling evaluation of the cytotoxic activity of podophyllotoxin analogues. 209-225
  
• Pekka Tiikkainen, Antti Poso, Olli-P. Kallioniemi:
  Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens. 227-239
  
• Phornphimon Maitarad, Sumalee Kamchonwongpaisan, Jarunee Vanichtanankul, Tirayut Vilaivan, Yongyuth Yuthavong, Supa Hannongbua:
  Interactions between cycloguanil derivatives and wild type and resistance-associated mutant Plasmodium falciparum dihydrofolate reductases. 241-252
  
• Josefin Rosén, Anders Lövgren, Thierry Kogej, Sorel Muresan, Johan Gottfries, Anders Backlund:
  ChemGPS-NP_Web: chemical space navigation online. 253-259
  

Volume 23, Number 5, May 2009

• Xiaoqing Liu, Zhilong Xiu, Ce Hao:
  Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation. 261-272
  
• Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan:
  Identifying conformational changes of the beta₂ adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. 273-288
  
• Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, Michael Feig:
  Scoring confidence index: statistical evaluation of ligand binding mode predictions. 289-299
  
• Bernhard Knapp, Ulrich Omasits, Sophie Frantal, Wolfgang Schreiner:
  A critical cross-validation of high throughput structural binding prediction methods for pMHC. 301-307
  
• Kazuya Nakao, Masaaki Fujikawa, Ryo Shimizu, Miki Akamatsu:
  QSAR application for the prediction of compound permeability with in silico descriptors in practical use. 309-319
  

Volume 23, Number 6, June 2009

• Xin Liu, Ming Kai, Lian Jin, Rui Wang:
  Computational study of the heterodimerization between µ and delta receptors. 321-332
  
• Ragothaman Yennamalli, Naidu Subbarao, Thorsten Kampmann, Ross P. McGeary, Paul R. Young, Bostjan Kobe:
  Identification of novel target sites and an inhibitor of the dengue virus E protein. 333-341
  
• Pubalee Sarmah, Ramesh C. Deka:
  DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect. 343-354
  
• Ajay N. Jain:
  Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. 355-374
  
• Chunquan Sheng, Haitao Ji, Zhenyuan Miao, Xiaoyin Che, Jianzhong Yao, Wenya Wang, Guoqiang Dong, Wei Guo, Jiaguo Lü, Wannian Zhang:
  Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design. 375-389
  

Volume 23, Number 7, July 2009

• Wendy A. Warr:
  CCDC well groomed: an interview with Colin Groom, Executive Director, Cambridge Crystallographic Data Centre, and Frank Allen, Emeritus Fellow. 391-394
  
• Jacob Kongsted, Pär Söderhjelm, Ulf Ryde:
  How accurate are continuum solvation models for drug-like molecules? 395-409
  
• Karen A. Rossi, Akbar Nayeem, Carolyn A. Weigelt, Stanley R. Krystek:
  Closing the side-chain gap in protein loop modeling. 411-418
  
• Gonçalo V. S. M. Carrera, Sunil Gupta, João Aires-de-Sousa:
  Machine learning of chemical reactivity from databases of organic reactions. 419-429
  
• Aihua Xie, Srinivas Odde, Sivaprakasam Prasanna, Robert J. Doerksen:
  Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationships and molecular docking. 431-448
  

Volume 23, Number 8, August 2009

• Diane Joseph-McCarthy:
  Challenges of fragment screening. 449-451
  
• Wendy A. Warr:
  Fragment-based drug discovery. 453-458
  
• Richard Law, Oliver Barker, John J. Barker, Thomas Hesterkamp, Robert Godemann, Ole Andersen, Tara Fryatt, Steve Courtney, Dave Hallett, Mark Whittaker:
  The multiple roles of computational chemistry in fragment-based drug design. 459-473
  
• Christian R. Schubert, Collin M. Stultz:
  The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design. 475-489
  
• Melissa R. Landon, Raquel L. Lieberman, Quyen Q. Hoang, Shulin Ju, Jose M. M. Caaveiro, Susan D. Orwig, Dima Kozakov, Ryan Brenke, Gwo-Yu Chuang, Dmitri Beglov, Sandor Vajda, Gregory A. Petsko, Dagmar Ringe:
  Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. 491-500
  
• Lars Neumann, Allegra Ritscher, Gerhard Müller, Doris Hafenbradl:
  Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology. 501-511
  
• Niklas Blomberg, David A. Cosgrove, Peter W. Kenny, Karin Kolmodin:
  Design of compound libraries for fragment screening. 513-525
  
• Sameer Kawatkar, Hongming Wang, Ryszard Czerminski, Diane Joseph-McCarthy:
  Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide. 527-539
  
• Kathryn Loving, Noeris K. Salam, Woody Sherman:
  Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. 541-554
  
• Rafael Gozalbes, Silvia Mosulén, Rodrigo J. Carbajo, Antonio Pineda-Lucena:
  Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors. 555-569
  
• Ksenia Oguievetskaia, Laetitia Martin-Chanas, Artem Vorotyntsev, Olivia Doppelt-Azeroual, Xavier Brotel, Stewart A. Adcock, Alexandre G. de Brevern, François Delfaud, Fabrice Moriaud:
  Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site. 571-582
  
• Anvita Gupta, Arun Kumar Gupta, Kothandaraman Seshadri:
  Structural models in the assessment of protein druggability based on HTS data. 583-592
  
• Andrea Zaliani, Krisztina Boda, Thomas Seidel, Achim Herwig, Christof H. Schwab, Johann Gasteiger, Holger Claussen, Christian Lemmen, Jörg Degen, Juri Pärn, Matthias Rarey:
  Second-generation de novo design: a view from a medicinal chemist perspective. 593-602
  
• I-Jen Chen, Roderick E. Hubbard:
  Lessons for fragment library design: analysis of output from multiple screening campaigns. 603-620
  

Volume 23, Number 9, September 2009

• Alexander S. Bayden, Micaela Fornabaio, J. Neel Scarsdale, Glen E. Kellogg:
  Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. 621-632
  
• Markus H. J. Seifert:
  Robust optimization of scoring functions for a target class. 633-644
  
• Mainak Guharoy, Pinak Chakrabarti:
  Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes. 645-654
  
• Shereena M. Arif, John D. Holliday, Peter Willett:
  Analysis and use of fragment-occurrence data in similarity-based virtual screening. 655-668
  
• Roberto Esposito, Giuseppe Ermondi, Giulia Caron:
  OpenCDLig: a free web application for sharing resources about cyclodextrin/ligand complexes. 669-675
  
• Austin B. Yongye, Yangmei Li, Marc A. Giulianotti, Yongping Yu, Richard A. Houghten, Karina Martínez-Mayorga:
  Modeling of peptides containing D-amino acids: implications on cyclization. 677-689
  

Volume 23, Number 10, October 2009

• Terry R. Stouch:
  The big problems don't go away by themselves. 691
  
• Yvonne C. Martin:
  Let's not forget tautomers. 693-704
  
• Zhigang Zhou, Yumin Li:
  Molecular dynamics simulation of S100B protein to explore ligand blockage of the interaction with p53 protein. 705-714
  
• Gwyn Skone, Irina Voiculescu, Stephen Cameron:
  Knowing when to give up: early-rejection stratagems in ligand docking. 715-724
  
• Joe Zhongxiang Zhou, Shenghua Shi, Jim Na, Zhengwei Peng, Tom Thacher:
  Combinatorial library-based design with Basis Products. 725-736
  
• Quan Chen, Wei Cui, Mingjuan Ji:
  Studies of chirality effect of 4-(phenylamino)-pyrrolo[2, 1-f][1, 2, 4]triazine on p38alpha by molecular dynamics simulations and free energy calculations. 737-745
  

Volume 23, Number 11, November 2009

• Stefano Costanzi, Irina G. Tikhonova, T. Kendall Harden, Kenneth A. Jacobson:
  Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands. 747-754
  
• Jun Gao, Zhijun Li:
  Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone. 755-763
  
• Robert D. Clark, Edmond J. Abrahamian:
  Using a staged multi-objective optimization approach to find selective pharmacophore models. 765-771
  
• Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
  Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. 773-784
  
• Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
  Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. 785-797
  
• Anna L. Bowman, Alexandros Makriyannis:
  Refined homology model of monoacylglycerol lipase: toward a selective inhibitor. 799-806
  
• Farag F. Sherbiny, Anke C. Schiedel, Astrid Maaß, Christa E. Müller:
  Homology modelling of the human adenosine A_2B receptor based on X-ray structures of bovine rhodopsin, the beta₂-adrenergic receptor and the human adenosine A_2A receptor. 807-828
  

Volume 23, Number 12, December 2009

• Terry R. Stouch:
  A well deserved honor: Yvonne Martin, 2009 recipient of the Herman Skolnik Award. 829-830
  
• Wendy A. Warr:
  Herman Skolnik award symposium honoring Yvonne Martin. 831-836
  
• M. Rami Reddy, Mark D. Erion:
  Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length. 837-843
  
• Francesco Strino, Jenn-Huei Lii, Hans-Joachim Gabius, Per-Georg Nyholm:
  Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics. 845-852
  
• Gregory J. Tawa, J. Christian Baber, Christine Humblet:
  Computation of 3D queries for ROCS based virtual screens. 853-868
  
• Bjoern A. Krueger, Tanja Weil, Gisbert Schneider:
  Comparative virtual screening and novelty detection for NMDA-Glycine_B antagonists. 869-881
  
• Luca A. Fenu, Ard Teisman, Stefan S. De Buck, Vikash K. Sinha, Ron A. H. J. Gilissen, Marjoleen J. M. A. Nijsen, Claire E. Mackie, Wendy E. Sanderson:
  Cardio-vascular safety beyond hERG: in silico modelling of a guinea pig right atrium assay. 883-895
  

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