Journal of Computer-Aided Molecular Design, Volume 29

Volume 29, Number 1, January 2015

Including Article of the Special Series: Statistics in Molecular Modeling

• 
  Gareth Jones:
  Fitting and handling dose response data. 1-11
• 
  Chaitanya A. K. Koppisetty, Martin Frank, Alexander Lyubartsev, Per-Georg Nyholm:
  Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations. 13-21
• 
  Stefano Della-Longa, Alessandro Arcovito:
  Intermediate states in the binding process of folic acid to folate receptor α: insights by molecular dynamics and metadynamics. 23-35
• 
  Cristian Celis-Barros, Leslie Saavedra-Rivas, J. Cristian Salgado, Bruce K. Cassels, Gerald Zapata-Torres:
  Molecular dynamics simulation of halogen bonding mimics experimental data for cathepsin L inhibition. 37-46
• 
  Andrea Schaller, Natalie K. Connors, Mirjana Dimitrijev Dwyer, Stefan A. Oelmeier, Jürgen Hubbuch, Anton P. J. Middelberg:
  Computational study of elements of stability of a four-helix bundle protein biosurfactant. 47-58
• 
  Ádám A. Kelemen, György G. Ferenczy, György M. Keserü:
  A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. 59-66
• 
  Ádám A. Kelemen, György G. Ferenczy, György M. Keserü:
  Erratum to: A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. 67
• 
  Yeng-Tseng Wang, Lea-Yea Chuang:
  Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach. 69-78
• 
  Steffen Lindert, Lorillee Tallorin, Quynh G. Nguyen, Michael D. Burkart, James Andrew McCammon:
  In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. 79-87
• 
  Sailu Sarvagalla, Vivek Kumar Singh, Yi-Yu Ke, Hui-Yi Shiao, Wen-Hsing Lin, Hsing-Pang Hsieh, John T. A. Hsu, Mohane Selvaraj Coumar:
  Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity. 89-100

Volume 29, Number 2, February 2015

• 
  Ann E. Cleves, Ajay N. Jain:
  Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes. 101-112
• 
  Magdalena Zwierzyna, Martin Vogt, Gerald M. Maggiora, Jürgen Bajorath:
  Design and characterization of chemical space networks for different compound data sets. 113-125
• 
  Sunanta Nabu, Chanin Nantasenamat, Wiwat Owasirikul, Ratana Lawung, Chartchalerm Isarankura-Na-Ayudhya, Maris Lapins, Jarl E. S. Wikberg, Virapong Prachayasittikul:
  Proteochemometric model for predicting the inhibition of penicillin-binding proteins. 127-141
• 
  Carlos Diaz, Ligia Llovera, Lorenzo Echevarria, Florencio E. Hernández:
  Assessment of the tautomeric population of benzimidazole derivatives in solution: a simple and versatile theoretical-experimental approach. 143-154
• 
  Sachin P. Patil, Michael F. Pacitti, Kevin S. Gilroy, John C. Ruggiero, Jonathan D. Griffin, Joseph J. Butera, Joseph M. Notarfrancesco, Shawn Tran, John W. Stoddart:
  Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study. 155-163
• 
  Daniel Cappel, Steven L. Dixon, Woody Sherman, Jianxin Duan:
  Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. 165-182
• 
  Katarina Nikolic, Lazaros Mavridis, Oscar M. Bautista-Aguilera, José Marco-Contelles, Holger Stark, Maria do Carmo Carreiras, Ilaria Rossi, Paola Massarelli, Danica Agbaba, Rona R. Ramsay, John B. O. Mitchell:
  Predicting targets of compounds against neurological diseases using cheminformatic methodology. 183-198

Volume 29, Number 3, March 2015

Including an Article of the Special Series: Statistics in Molecular Modeling

• 
  C. David Andersson, J. Mikael Hillgren, Cecilia M. Lindgren, Weixing Qian, Christine Akfur, Lotta Berg, Fredrik Ekström, Anna Linusson:
  Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase. 199-215
• 
  Caroline C. Zanith, Josefredo R. Pliego Jr.:
  Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile. 217-224
• 
  Vedat Durmaz:
  Markov model-based polymer assembly from force field-parameterized building blocks. 225-232
• 
  Gleb V. Sitnikov, Nelly I. Zhokhova, Yury A. Ustynyuk, Alexandre Varnek, Igor I. Baskin:
  Continuous indicator fields: a novel universal type of molecular fields. 233-247
• 
  Seneha Santoshi, Naresh Kumar Manchukonda, Charu Suri, Manya Sharma, Balasubramanian Sridhar, Silja Joseph, Manu Lopus, Srinivas Kantevari, Iswar Baitharu, Pradeep Kumar Naik:
  Rational design of biaryl pharmacophore inserted noscapine derivatives as potent tubulin binding anticancer agents. 249-270
• 
  Joséphine Abi-Ghanem, Sergey A. Samsonov, M. Teresa Pisabarro:
  Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility. 271-282
• 
  Manas Mondal, Devapriya Choudhury, Jaydeb Chakrabarti, Dhananjay Bhattacharyya:
  Role of indirect readout mechanism in TATA box binding protein-DNA interaction. 283-295

Volume 29, Number 4, April 2015

• 
  Wendy A. Warr:
  App-etite for change. 297-303
• 
  Roman Garnett, Thomas Gärtner, Martin Vogt, Jürgen Bajorath:
  Introducing the 'active search' method for iterative virtual screening. 305-314
• 
  Emilio Gallicchio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi A. Pethe, Jie Zhu, Ronald M. Levy:
  BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. 315-325
• 
  Ignacio Aliagas, Alberto Gobbi, Timothy Heffron, Man-Ling Lee, Daniel F. Ortwine, Mark Zak, S. Cyrus Khojasteh:
  A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery. 327-338
• 
  Hyun-Jin Kang, Hyun-Ju Park:
  In silico identification of novel ligands for G-quadruplex in the c-MYC promoter. 339-348
• 
  Yu Wang, Yanzhi Guo, Qifan Kuang, Xuemei Pu, Yue Ji, Zhihang Zhang, Menglong Li:
  A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach. 349-360
• 
  Alessia Visconti, Giuseppe Ermondi, Giulia Caron, Roberto Esposito:
  Prediction and interpretation of the lipophilicity of small peptides. 361-370
• 
  Balasubramanian Sangeetha, Muthukumaran Rajagopalan, Amutha Ramaswamy:
  Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase. 371-385

Volume 29, Number 5, May 2015

Including an Article of the Special Series: Statistics in Molecular Modeling

• 
  Eric Martin, Eddie Cao:
  Euclidean chemical spaces from molecular fingerprints: Hamming distance and Hempel's ravens. 387-395
• 
  Pavel V. Klimovich, Michael R. Shirts, David L. Mobley:
  Guidelines for the analysis of free energy calculations. 397-411
• 
  Rajan Chaudhari, Andrew J. Heim, Zhijun Li:
  Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions. 413-420
• 
  Stephanie N. Lewis, Zulma Garcia, Raquel Hontecillas, Josep Bassaganya-Riera, David R. Bevan:
  Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands. 421-439
• 
  Jacopo Sgrignani, Beatrice Novati, Giorgio Colombo, Giovanni Grazioso:
  Covalent docking of selected boron-based serine beta-lactamase inhibitors. 441-450
• 
  Eleonora Gianti, Randy J. Zauhar:
  An SH2 domain model of STAT5 in complex with phospho-peptides define "STAT5 Binding Signatures". 451-470
• 
  Xueli Zhang, Xuedong Gong:
  A simple, fast and convenient new method for predicting the stability of nitro compounds. 471-483

Volume 29, Number 6, June 2015

• 
  Ann E. Cleves, Ajay N. Jain:
  Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. 485-509
• 
  Jianwen A. Feng, Ignacio Aliagas, Philippe Bergeron, Jeffrey M. Blaney, Erin K. Bradley, Michael F. T. Koehler, Man-Ling Lee, Daniel F. Ortwine, Vickie Tsui, Johnny Wu, Alberto Gobbi:
  An integrated suite of modeling tools that empower scientists in structure- and property-based drug design. 511-523
• 
  Emilie Pihan, Roberto F. Delgadillo, Michelle L. Tonkin, Martine Pugnière, Maryse Lebrun, Martin J. Boulanger, Dominique Douguet:
  Computational and biophysical approaches to protein-protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex. 525-539
• 
  Andrej Perdih, Martina Hrast, Kaja Pureber, Hélène Barreteau, Simona Golic Grdadolnik, Darko Kocjan, Stanislav Gobec, Tomaz Solmajer, Gerhard Wolber:
  Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization. 541-560
• 
  Nour Jamal Jaradat, Mohammad A. Khanfar, Maha Habash, Mutasem Omar Taha:
  Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors. 561-581

Volume 29, Number 7, July 2015

Including an Article of the Special Series: Statistics in Molecular Modeling

• 
  Ullrika Sahlin:
  Assessment of uncertainty in chemical models by Bayesian probabilities: Why, when, how? 583-594
• 
  Bijun Zhang, Martin Vogt, Gerald M. Maggiora, Jürgen Bajorath:
  Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity. 595-608
• 
  Barbara Kalinowska, Piotr Fabian, Katarzyna Stapor, Irena Roterman:
  Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. 609-618
• 
  Yan Li, Michel Delamar, Patricia Busca, Guillaume Prestat, Laurent Le Corre, Laurence Legeai-Mallet, Rongjing Hu, Ruisheng Zhang, Florent Barbault:
  Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3). 619-641
• 
  H. Bauke Albada, Eyal Golub, Itamar Willner:
  Computational docking simulations of a DNA-aptamer for argininamide and related ligands. 643-654
• 
  Hulya Unan, Ahmet Yildirim, Mustafa Tekpinar:
  Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field. 655-665
• 
  David Fernández, Joaquín Ortega-Castro, Laura Mariño, Joan Perelló, Juan Frau:
  Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition. 667-680

Volume 29, Number 8, August 2015

• 
  Wendy A. Warr:
  Many InChIs and quite some feat. 681-694
• 
  Antonio de la Vega de León, Shilva Kayastha, Dilyana Dimova, Thomas Schultz, Jürgen Bajorath:
  Visualization of multi-property landscapes for compound selection and optimization. 695-705
• 
  Mitja Ogrizek, Samo Turk, Samo Lesnik, Izidor Sosic, Milan Hodoscek, Bojana Mirkovic, Janko Kos, Dusanka Janezic, Stanislav Gobec, Janez Konc:
  Molecular dynamics to enhance structure-based virtual screening on cathepsin B. 707-712
• 
  Heloisa dos Santos Muniz, Alessandro S. Nascimento:
  Ligand- and receptor-based docking with LiBELa. 713-723
• 
  Jennifer M. Smith, Christopher N. Rowley:
  Automated computational screening of the thiol reactivity of substituted alkenes. 725-735
• 
  Silvia Paoletta, Davide Sabbadin, Ivar von Kügelgen, Sonja Hinz, Vsevolod Katritch, Kristina Hoffmann, Aliaa Abdelrahman, Jens Straßburger, Younis Baqi, Qiang Zhao, Raymond C. Stevens, Stefano Moro, Christa E. Müller, Kenneth A. Jacobson:
  Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information. 737-756
• 
  Rino Ragno, Flavio Ballante, Adele Pirolli, Richard B. Wickersham III, Alexandros Patsilinakos, Stéphanie Hesse, Enrico Perspicace, Gilbert Kirsch:
  Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches. 757-776

Volume 29, Number 9, September 2015

Special Issue on Data Part 2: Experimental Data

• 
  Christian Kramer, John D. Chodera, Terry R. Stouch:
  Introduction to the special issue: Data Part 2: Experimental Data. 777
• 
  Nicola Colclough, Mark C. Wenlock:
  Interpreting physicochemical experimental data sets. 779-794
• 
  Susanne Winiwarter, Brian Middleton, Barry Jones, Paul Courtney, Bo Lindmark, Ken M. Page, Alan Clark, Claire Landqvist:
  Time dependent analysis of assay comparability: a novel approach to understand intra- and inter-site variability over time. 795-807
• 
  Matthew D. Segall, Edmund J. Champness:
  The challenges of making decisions using uncertain data. 809-816
• 
  Marc C. Deller, Bernhard Rupp:
  Models of protein-ligand crystal structures: trust, but verify. 817-836
• 
  J. Peter Guthrie:
  Presenting data in such a fashion that they can be used by other scientists. 837-846
• 
  Hermann Wätzig, Imke Oltmann-Norden, Franziska Steinicke, Hassan A. Alhazmi, Markus Nachbar, Deia Abd El-Hady, Hassan M. Albishri, Knut Baumann, Thomas E. Exner, Frank M. Boeckler, Sami El Deeb:
  Data quality in drug discovery: the role of analytical performance in ligand binding assays. 847-865
• 
  Stefan G. Krimmer, Gerhard Klebe:
  Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. 867-883
• 
  George Papadatos, Anna Gaulton, Anne Hersey, John P. Overington:
  Activity, assay and target data curation and quality in the ChEMBL database. 885-896
• 
  Marvin Waldman, Robert Fraczkiewicz, Robert D. Clark:
  Tales from the war on error: the art and science of curating QSAR data. 897-910
• 
  Bernd Beck, Daniel Seeliger, Jan M. Kriegl:
  The impact of data integrity on decision making in early lead discovery. 911-921

Volume 29, Number 10, October 2015

Including an Article of the Special Series: Statistics in Molecular Modeling

• 
  Mark McGann, Anthony Nicholls, Istvan J. Enyedy:
  The statistics of virtual screening and lead optimization. 923-936
• 
  Bijun Zhang, Martin Vogt, Gerald M. Maggiora, Jürgen Bajorath:
  Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. 937-950
• 
  David Adrian Saez, Esteban Vöhringer-Martinez:
  A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation. 951-961
• 
  Anthony R. Bradley, Ian D. Wall, Frank von Delft, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden:
  WONKA: objective novel complex analysis for ensembles of protein-ligand structures. 963-973
• 
  Motonori Tsuji, Koichi Shudo, Hiroyuki Kagechika:
  Docking simulations suggest that all-trans retinoic acid could bind to retinoid X receptors. 975-988
• 
  Sanna P. Niinivehmas, Kari Salokas, Sakari Lätti, Hannu Raunio, Olli T. Pentikäinen:
  Ultrafast protein structure-based virtual screening with Panther. 989-1006

Volume 29, Number 11, November 2015

• 
  Pavel V. Klimovich, David L. Mobley:
  A Python tool to set up relative free energy calculations in GROMACS. 1007-1014
• 
  David J. Diller, Nancy D. Connell, William J. Welsh:
  Avalanche for shape and feature-based virtual screening with 3D alignment. 1015-1024
• 
  Romain M. Wolf:
  Extracting ligands from receptors by reversed targeted molecular dynamics. 1025-1034
• 
  Chunli Pang, Hong-Bo Yuan, Tianguang Cao, Ji-Guo Su, Ya-Fei Chen, Hui Liu, Hui Yu, Hai-Ling Zhang, Yong Zhan, Hailong An, Yue-Bin Han:
  Molecular simulation assisted identification of Ca2+ binding residues in TMEM16A. 1035-1043
• 
  Yan Li, Xiang Li, Zigang Dong:
  Statistical analysis of EGFR structures' performance in virtual screening. 1045-1055
• 
  Gaurao V. Dhoke, Christoph Loderer, Mehdi D. Davari, Marion Ansorge-Schumacher, Ulrich Schwaneberg, Marco Bocola:
  Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment. 1057-1069
• 
  Bijun Zhang, Martin Vogt, Gerald M. Maggiora, Jürgen Bajorath:
  Erratum to: Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. 1071-1072

Volume 29, Number 12, December 2015

Including an Article of the Special Series: Statistics in Molecular Modeling

• 
  Sonya M. Hanson, Sean Ekins, John D. Chodera:
  Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. 1073-1086
• 
  Pavel Sidorov, Héléna A. Gaspar, Gilles Marcou, Alexandre Varnek, Dragos Horvath:
  Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds. 1087-1108
• 
  Katarina Roos, Anders Hogner, Derek Ogg, Martin J. Packer, Eva Hansson, Kenneth L. Granberg, Emma Evertsson, Anneli Nordqvist:
  Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods. 1109-1122
• 
  Tingting Feng, Yanjun Zhang, Jing-Na Ding, Song Fan, Ju-Guang Han:
  Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation. 1123-1136
• 
  Márton Vass, Balázs Jójárt, Ferenc Bogár, Gábor Paragi, György M. Keserü, Ákos Tarcsay:
  Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor. 1137-1149
• 
  Zakaria Alamiddine, Balaji Selvam, José Pedro Cerón-Carrasco, Monique Mathé-Allainmat, Jacques Lebreton, Steeve H. Thany, Adèle D. Laurent, Jérôme Graton, Jean-Yves Le Questel:
  Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation. 1151-1167