Journal of Computer-Aided Molecular Design, Volume 26

Volume 26, Number 1, January 2012

Special Issue: The next 25 years: Commemorating the 25th anniversary of the Journal of Computer-Aided Molecular Design

• 
  Terry R. Stouch:
  Looking forward into the next 25 years: the 25th anniversary issue of the Journal of Computer-Aided Molecular Design. 1
• 
  Garland R. Marshall:
  Limiting assumptions in structure-based design: binding entropy. 3-8
• 
  Ruben Abagyan:
  Computational chemistry in 25 years. 9-10
• 
  Jürgen Bajorath:
  Computational chemistry in pharmaceutical research: at the crossroads. 11-12
• 
  Jeff Blaney:
  A very short history of structure-based design: how did we get here and where do we need to go? 13-14
• 
  David W. Borhani, David E. Shaw:
  The future of molecular dynamics simulations in drug discovery. 15-26
• 
  Frank K. Brown:
  Democratization of computational chemistry and Chem(o)informatics. 27-28
• 
  Robert D. Clark, Marvin Waldman:
  Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design. 29-34
• 
  Richard D. Cramer:
  The inevitable QSAR renaissance. 35-38
• 
  Yufeng J. Tseng, Anton J. Hopfinger, Emilio Xavier Esposito:
  The great descriptor melting pot: mixing descriptors for the common good of QSAR models. 39-43
• 
  Federico Gago:
  Reflections on the past 25 years. 45
• 
  Robert C. Glen:
  Computational chemistry and cheminformatics: an essay on the future. 47-49
• 
  Darren V. S. Green, Andrew R. Leach, Martha S. Head:
  Computer-aided molecular design under the SWOTlight. 51-56
• 
  Ajay N. Jain, Ann E. Cleves:
  Does your model weigh the same as a Duck? 57-67
• 
  Peter W. Kenny:
  Computation, experiment and molecular design. 69-72
• 
  Irwin D. Kuntz:
  Darwinian Docking. 73-75
• 
  Eric J. Martin, Peter Ertl, Peter Hunt, José S. Duca, Richard Lewis:
  Gazing into the crystal ball; the future of computer-aided drug design. 77-79
• 
  Xavier Barril, F. Javier Luque:
  Molecular simulation methods in drug discovery: a prospective outlook. 81-86
• 
  Gerald M. Maggiora:
  Is there a future for computational chemistry in drug research? 87-90
• 
  Yvonne C. Martin, Steven W. Muchmore:
  Frozen out: molecular modeling in the age of cryocrystallography. 91-92
• 
  David L. Mobley:
  Let's get honest about sampling. 93-95
• 
  Mark A. Murcko, W. Patrick Walters:
  Alpha shock. 97-102
• 
  Anthony Nicholls:
  The character of molecular modeling. 103-105
• 
  Tudor I. Oprea, Olivier Taboureau, Cristian Bologa:
  Of possible cheminformatics futures. 107-112
• 
  Matthias Rarey:
  Some thoughts on the "A" in computer-aided molecular design. 113-114
• 
  Gisbert Schneider:
  Designing the molecular future. 115-120
• 
  Matthew D. Segall:
  Can we really do computer-aided drug design? 121-124
• 
  Terry R. Stouch:
  The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years. 125-134
• 
  Igor V. Tetko:
  The perspectives of computational chemistry modeling. 135-136
• 
  G. Seddon, Valère Lounnas, Ross McGuire, T. van den Bergh, Robert P. Bywater, Laerte Oliveira, Gert Vriend:
  Drug design for ever, from hype to hope. 137-150
• 
  Wendy A. Warr:
  Silver threads. 151-152
• 
  Peter Willett:
  The Journal of Computer-Aided Molecular Design: a bibliometric note. 153-157
• 
  Walter S. Woltosz:
  If we designed airplanes like we design drugs... 159-163

Volume 26, Number 2, February 2012

• 
  Wendy A. Warr:
  An interview with Phil Bourne, associate director of the RCSB protein data bank. 165-167
• 
  John W. Liebeschuetz, Jana Hennemann, Tjelvar S. G. Olsson, Colin R. Groom:
  The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. 169-183
• 
  Oliver Korb, Tim ten Brink, Fredrick Robin Devadoss, Victor Paul Raj, Matthias Keil, Thomas E. Exner:
  Are predefined decoy sets of ligand poses able to quantify scoring function accuracy? 185-197
• 
  Jenn-Huei Lii, Ching-Han Hu:
  An improved theoretical approach to the empirical corrections of density functional theory. 199-213
• 
  Parimal Kar, Volker Knecht:
  Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. 215-232
• 
  Pradeep Kumar Naik, Manu Lopus, Ritu Aneja, Surya N. Vangapandu, Harish C. Joshi:
  In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin). 233-247
• 
  Rand Shahin, Saja AlQtaishat, Mutasem O. Taha:
  Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors. 249-266

Volume 26, Number 3, March 2012

• 
  Deepak Lokwani, Reecha Shah, Santosh Mokale, Padma Shastry, Devanand Shinde:
  Development of energetic pharmacophore for the designing of 1, 2, 3, 4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2 inhibitors. 267-277
• 
  Ammar Abdo, Faisal Saeed, Hamza Hentabli, Ali Ahmed, Naomie Salim:
  Ligand expansion in ligand-based virtual screening using relevance feedback. 279-287
• 
  Amit Kumar Chaubey, Kshatresh Dutta Dubey, Rajendra Prasad Ojha:
  Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. 289-299
• 
  Andrew J. Heim, Zhijun Li:
  Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. 301-309
• 
  Gijs Schaftenaar, Jacob de Vlieg:
  Quantum mechanical polar surface area. 311-318
• 
  Álvaro Cortés Cabrera, Federico Gago, Antonio Morreale:
  A reverse combination of structure-based and ligand-based strategies for virtual screening. 319-327
• 
  Hao Xu, Wenxiao Pan, Ruoxi Wang, Dongju Zhang, Chengbu Liu:
  Understanding the mechanism of cellulose dissolution in 1-butyl-3-methylimidazolium chloride ionic liquid via quantum chemistry calculations and molecular dynamics simulations. 329-337
• 
  Liang-Tsung Huang, M. Michael Gromiha:
  Real value prediction of protein folding rate change upon point mutation. 339-347
• 
  Razieh Sabet, Afshin Fassihi, Bahram Hemmateenejad, Lotfollah Saghaie, Ramin Miri, Maryam Gholami:
  Computer-aided design of novel antibacterial 3-hydroxypyridine-4-ones: application of QSAR methods based on the MOLMAP approach. 349-361
• 
  H.-H. Wu, C.-C. Chen, Chi-Ming Chen:
  Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. 363-374

Volume 26, Number 4, April 2012

• 
  Jeyasigamani F. A. Selvin, Thanu R. K. Priyadarzini, Kasinadar Veluraja:
  Sialyldisaccharide conformations: a molecular dynamics perspective. 375-385
• 
  Michael A. Johnston, Damien Farrell, Jens Erik Nielsen:
  A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. 387-396
• 
  Joseph R. André, Marie-Jeanne Clément, Elisabeth Adjadj, Flavio Toma, Patrick A. Curmi, Philippe Manivet:
  The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament. 397-407
• 
  Natalie B. Vinh, Jamie S. Simpson, Peter J. Scammells, David K. Chalmers:
  Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK. 409-423
• 
  Jacopo Sgrignani, Alessandra Magistrato, Matteo Dal Peraro, Alejandro J. Vila, Paolo Carloni, Roberta Pierattelli:
  On the active site of mononuclear B1 metallo β-lactamases: a computational study. 425-435
• 
  Anders Poulsen, Anthony William, Stéphanie Blanchard, Angeline Lee, Harish Nagaraj, Haishan Wang, Eeling Teo, Evelyn Tan, Kee Chuan Goh, Brian Dymock:
  Structure-based design of oxygen-linked macrocyclic kinase inhibitors: discovery of SB1518 and SB1578, potent inhibitors of Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3). 437-450
• 
  Robin Taylor, Jason C. Cole, David A. Cosgrove, Eleanor J. Gardiner, Valerie J. Gillet, Oliver Korb:
  Development and validation of an improved algorithm for overlaying flexible molecules. 451-472

Volume 26, Number 5, May 2012

Special Issue: SAMPL3: Blinded prediction of host-guest binding, hydration energies, and trypsin inhibition

• 
  A. Geoffrey Skillman:
  SAMPL3: blinded prediction of host-guest binding affinities, hydration free energies, and trypsin inhibitors. 473-474
• 
  Hari S. Muddana, C. Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson:
  Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. 475-487
• 
  Matthew T. Geballe, J. Peter Guthrie:
  The SAMPL3 blind prediction challenge: transfer energy overview. 489-496
• 
  Janet Newman, Olan Dolezal, Vincent Fazio, Tom Caradoc-Davies, Thomas S. Peat:
  The DINGO dataset: a comprehensive set of data for the SAMPL challenge. 497-503
• 
  Emilio Gallicchio, Ronald M. Levy:
  Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). 505-516
• 
  Hari S. Muddana, Michael K. Gilson:
  Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. 517-525
• 
  Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde:
  Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. 527-541
• 
  Gerhard König, Bernard R. Brooks:
  Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. 543-550
• 
  David L. Mobley, Shaui Liu, David S. Cerutti, William C. Swope, Julia E. Rice:
  Alchemical prediction of hydration free energies for SAMPL. 551-562
• 
  Charles W. Kehoe, Christopher J. Fennell, Ken A. Dill:
  Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. 563-568
• 
  Morgan Lawrenz, Jeff Wereszczynski, Juan Manuel Ortiz-Sánchez, Sara E. Nichols, James Andrew McCammon:
  Thermodynamic integration to predict host-guest binding affinities. 569-576
• 
  Nobuko Hamaguchi, Laszlo Fusti-Molnar, Stanislaw Wlodek:
  Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes. 577-582
• 
  John L. Kulp III, Seth N. Blumenthal, Qiang Wang, Richard L. Bryan, Frank Guarnieri:
  A fragment-based approach to the SAMPL3 Challenge. 583-594
• 
  Georgiana Surpateanu, Bogdan I. Iorga:
  Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. 595-601
• 
  Ashutosh Kumar, Kam Y. J. Zhang:
  Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge. 603-616
• 
  Traian Sulea, Hervé Hogues, Enrico O. Purisima:
  Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction. 617-633
• 
  Oliver Beckstein, Bogdan I. Iorga:
  Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. 635-645
• 
  Mark L. Benson, John C. Faver, Melek N. Ucisik, Danial S. Dashti, Zheng Zheng, Kenneth M. Merz Jr.:
  Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. 647-659
• 
  Traian Sulea, Enrico O. Purisima:
  Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models. 661-667
• 
  Jens Reinisch, Andreas Klamt, Michael Diedenhofen:
  Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set. 669-673

Volume 26, Number 6, June 2012

Special Issue: A snapshot in time: Docking Challenge

• 
  Marco A. C. Neves, Maxim Totrov, Ruben Abagyan:
  Docking and scoring with ICM: the benchmarking results and strategies for improvement. 675-686
• 
  Russell Spitzer, Ajay N. Jain:
  Surflex-Dock: Docking benchmarks and real-world application. 687-699
• 
  Nadine Schneider, Sally A. Hindle, Gudrun Lange, Robert Klein, Jürgen Albrecht, Hans Briem, Kristin Beyer, Holger Claußen, Marcus Gastreich, Christian Lemmen, Matthias Rarey:
  Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. 701-723
• 
  Fedor N. Novikov, Viktor S. Stroylov, Alexey A. Zeifman, Oleg V. Stroganov, Val Kulkov, Ghermes G. Chilov:
  Lead Finder docking and virtual screening evaluation with Astex and DUD test sets. 725-735
• 
  John W. Liebeschuetz, Jason C. Cole, Oliver Korb:
  Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test. 737-748
• 
  Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo:
  Evaluation of DOCK 6 as a pose generation and database enrichment tool. 749-773
• 
  Christopher R. Corbeil, Christopher I. Williams, Paul Labute:
  Variability in docking success rates due to dataset preparation. 775-786
• 
  Matthew P. Repasky, Robert B. Murphy, Jay L. Banks, Jeremy R. Greenwood, Ivan Tubert-Brohman, Sathesh Bhat, Richard A. Friesner:
  Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide. 787-799

Volume 26, Number 7, July 2012

• 
  Wendy A. Warr:
  Scientific workflow systems: Pipeline Pilot and KNIME. 801-804
• 
  Richard D. Cramer:
  R-group template CoMFA combines benefits of "ad hoc" and topomer alignments using 3D-QSAR for lead optimization. 805-819
• 
  Márton Vass, Ákos Tarcsay, György M. Keserü:
  Multiple ligand docking by Glide: implications for virtual second-site screening. 821-834
• 
  Jerez A. Te, Maoqing Dong, Laurence J. Miller, Andrew J. Bordner:
  Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists. 835-845
• 
  Sanjay K. Upadhyay, Yellamraju U. Sasidhar:
  Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes. 847-864
• 
  Arijit Basu, Barij N. Sinha:
  Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access. 865-881
• 
  Grigorios Skolidis, Katja Hansen, Guido Sanguinetti, Matthias Rupp:
  Multi-task learning for pKa prediction. 883-895

Volume 26, Number 8, August 2012

• 
  Mark McGann:
  FRED and HYBRID docking performance on standardized datasets. 897-906
• 
  Flavio Ballante, Ira Musmuca, Garland R. Marshall, Rino Ragno:
  Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. 907-919
• 
  Sameer Kawatkar, Demetri Moustakas, Matthew Miller, Diane Joseph-McCarthy:
  Virtual fragment screening: exploration of MM-PBSA re-scoring. 921-934
• 
  Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Stefan Zahn, Frank M. Boeckler:
  Using halogen bonds to address the protein backbone: a systematic evaluation. 935-945
• 
  Aizi Nor Mazila Ramli, Nor Muhammad Mahadi, Mohd Shahir Shamsir, Amir Rabu, Kwee Hong Joyce-Tan, Abdul Munir Abdul Murad, Rosli Md. Illias:
  Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. 947-961
• 
  Liang Xu, Ke Gao, Chunyu Bao, Xicheng Wang:
  Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules. 963-976
• 
  Omar Alvarado, Gonzalo A. Jaña, Eduardo J. Delgado:
  Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP. 977-982
• 
  Hwangseo Park, Seunghee Hong, Sungwoo Hong:
  Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening. 983-992

Volume 26, Number 9, September 2012

• 
  Terry R. Stouch:
  Our gratitude to outgoing Editor-in-Chief Andrew Leach and a hearty welcome to new Editor-in-Chief, Richards Lewis. 993
• 
  Álvaro Cortés Cabrera, Antonio Morreale, Federico Gago, Celerino Abad-Zapatero:
  AtlasCBS: a web server to map and explore chemico-biological space. 995-1003
• 
  Ana Negri, Jihong Li, Sarasija Naini, Barry S. Coller, Marta Filizola:
  Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand. 1005-1015
• 
  Sandeep Modi, Jin Li, Sophie Malcomber, Claire Moore, Andrew D. Scott, Andrew White, Paul L. Carmichael:
  Integrated in silico approaches for the prediction of Ames test mutagenicity. 1017-1033
• 
  Giovanni Grazioso, Laura Legnani, Lucio Toma, Roberta Ettari, Nicola Micale, Carlo De Micheli:
  Mechanism of falcipain-2 inhibition by α, β-unsaturated benzo[1, 4]diazepin-2-one methyl ester. 1035-1043
• 
  Agata Martyniak, Jaroslaw J. Panek, Aneta Jezierska-Mazzarello, Aleksander Filarowski:
  Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines. 1045-1053
• 
  Euzébio G. Barbosa, Kerly F. M. Pasqualoto, Márcia M. C. Ferreira:
  The receptor-dependent LQTA-QSAR: application to a set of trypanothione reductase inhibitors. 1055-1065
• 
  Angusamy Annapoorani, Venugopal Umamageswaran, Radhakrishnan Parameswari, Shunmugiah Karutha Pandian, Arumugam Veera Ravi:
  Computational discovery of putative quorum sensing inhibitors against LasR and RhlR receptor proteins of Pseudomonas aeruginosa. 1067-1077
• 
  Mats Linder, Adam Johannes Johansson, Tjelvar S. G. Olsson, John W. Liebeschuetz, Tore Brinck:
  Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics. 1079-1095

Volume 26, Number 10, October 2012

• 
  Anthony Nicholls:
  Call for Papers: GRC, CADD, and statistics, and all that. 1097-1099
• 
  Ruifang Li, Jürgen Bajorath:
  Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening. 1101-1109
• 
  Nicolas Galland, Soleymane Kone, Jean-Yves Le Questel:
  Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. 1111-1126
• 
  Wee Kiang Yeo, Mei Lin Go, Shahul Nilar:
  Extraction and validation of substructure profiles for enriching compound libraries. 1127-1141
• 
  Ingemar Nilsson, Magnus O. Polla:
  Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: Renaissance of the Free-Wilson methodology. 1143-1157
•