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