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ORCIDJournal of Computer-Aided Molecular Design, Volume 25
Volume 25, Number 1, January 2011
- Alpeshkumar K. Malde
, Alan E. Mark:
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. 1-12 - Markus A. Lill, Matthew L. Danielson:
Computer-aided drug design platform using PyMOL. 13-19 - Cristina Rodríguez-Rodríguez, Albert Rimola, Jorge Alí-Torres, Mariona Sodupe, Pilar González-Duarte:
In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases. 21-30 - Vladimir Frecer, Pierfausto Seneci, Stanislav Miertus:
Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. 31-49 - Maria Elena Silva, Ralf Heim, Andrea Straßer, Sigurd Elz, Stefan Dove:
Theoretical studies on the interaction of partial agonists with the 5-HT2A receptor. 51-66 - Dongsheng Cao, Yizeng Liang, Qingsong Xu, Yifeng Yun, Hongdong Li:
Toward better QSAR/QSPR modeling: simultaneous outlier detection and variable selection using distribution of model features. 67-80 - Zaheer-ul-Haq, Waqasuddin Khan:
Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs. 81-101
Volume 25, Number 2, February 2011
- Wendy A. Warr:
Guiding effective decisions: an interview with Matthew Segall, CEO of Optibrium. 103-106 - Rasmus K. Petersen, Kathrine B. Christensen, Andreana N. Assimopoulou, Xavier Fretté, Vassilios P. Papageorgiou, Karsten Kristiansen, Irene Kouskoumvekaki:
Pharmacophore-driven identification of PPARγ agonists from natural sources. 107-116 - Katarzyna Prymula, Tomasz Jadczyk, Irena Roterman:
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. 117-133 - Shiri Stempler, Michal Levy-Sakin, Anat Frydman-Marom, Yaniv Amir, Roni Scherzer-Attali, Ludmila Buzhansky, Ehud Gazit, Hanoch Senderowitz:
Quantitative structure-activity relationship analysis of β-amyloid aggregation inhibitors. 135-144 - M. Alcolea Palafox, P. Posada-Moreno, Antonio Luis Villarino-Marín, C. Martinez-Rincon, I. Ortuño-Soriano, I. Zaragoza-García:
DFT calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O. 145-161 - Sébastien Dilly, Jean-François Liégeois:
Interaction of clozapine and its nitrenium ion with rat D2 dopamine receptors: in vitro binding and computational study. 163-169 - Yuanhua Cheng, Wei Cui, Quan Chen, Chen-Ho Tung, Mingjuan Ji, Fushi Zhang:
The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations. 171-180 - Mattia Falconi, Francesco Oteri, Francesco Di Palma, Saurabh Kumar Pandey, Andrea Battistoni, Alessandro Desideri:
Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport. 181-194
Volume 25, Number 3, March 2011
- Yvonne C. Martin:
Why you should read Dr. Cramer's perspective. 195-196 - Richard D. Cramer:
Rethinking 3D-QSAR. 197-201 - Matthew B. Stocks, Stephen D. Laycock, Steven Hayward:
Applying forces to elastic network models of large biomolecules using a haptic feedback device. 203-211 - Ge-Fei Hao, Ying Tan, Ning-Xi Yu, Guangfu Yang:
Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations. 213-222 - Petr Dobes, Jindrich Fanfrlík, Jan Rezác, Michal Otyepka, Pavel Hobza:
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. 223-235 - Dragos Horvath, Christian J. Koch, Gisbert Schneider, Gilles Marcou, Alexandre Varnek:
Local neighborhood behavior in a combinatorial library context. 237-252 - Alexander Bujotzek, Min Shan, Rainer Haag, Marcus Weber:
Towards a rational spacer design for bivalent inhibition of estrogen receptor. 253-262 - Tim Knehans, Andreas Schüller, Danny N. Doan, Kassoum Nacro, Jeffrey Hill, Peter Güntert, M. S. Madhusudhan, Tanja Weil, Subhash G. Vasudevan:
Structure-guided fragment-based in silico drug design of dengue protease inhibitors. 263-274 - Nikita Chopra, Shivangi Agarwal, Shashikala Verma, Sonika Bhatnagar, Rakesh Bhatnagar:
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. 275-291
Volume 25, Number 4, April 2011
- Terry R. Stouch, Yvonne C. Martin:
A giant's shoulders: a Perspective from Professor Norman L. Allinger. 293-294 - Norman L. Allinger:
Understanding molecular structure from molecular mechanics. 295-316 - Jin Hee Lee, Yoonji Lee, HyungChul Ryu, Dong Wook Kang, Jeewoo Lee, Jozsef Lazar, Larry V. Pearce, Vladimir A. Pavlyukovets, Peter M. Blumberg, Sun Choi:
Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies. 317-327 - Francesca Deflorian, Kenneth A. Jacobson:
Comparison of three GPCR structural templates for modeling of the P2Y12 nucleotide receptor. 329-338 - Eunkyoung Jung, Seung-Hoon Choi, Nam-Kyung Lee, Sang-Kee Kang, Yun-Jaie Choi, Jae-Min Shin, Kihang Choi, Dong Hyun Jung:
Machine learning study for the prediction of transdermal peptide. 339-347 - Julio Caballero, Miguel Quiliano, Jans H. Alzate-Morales, Mirko Zimic, Eric Deharo:
Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-f][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors. 349-369 - Yunierkis Pérez-Castillo, Matheus Froeyen, Miguel Ángel Cabrera-Pérez, Ann Nowé:
Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling. 371-393
Volume 25, Number 5, May 2011
- Xevi Biarnés, Salvatore Bongarzone, Attilio Vittorio Vargiu, Paolo Carloni, Paolo Ruggerone:
Molecular motions in drug design: the coming age of the metadynamics method. 395-402 - Sandhya Kortagere, Ernest Mui, Rima McLeod, William J. Welsh:
Rapid discovery of inhibitors of Toxoplasma gondii using hybrid structure-based computational approach. 403-411 - Dilraj Lama, Ramasubbu Sankararamakrishnan:
Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-XL. 413-426 - Barry Robson, Jin Li, Richard Dettinger, Amanda E. Peters, Stephen K. Boyer:
Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations. 427-441 - Pradeep Kumar Naik, Biswa Prasun Chatterji, Surya N. Vangapandu, Ritu Aneja, Ramesh Chandra, Srinivas Kanteveri, Harish C. Joshi:
Rational design, synthesis and biological evaluations of amino-noscapine: a high affinity tubulin-binding noscapinoid. 443-454 - Pankaj Kumar, Xiao Hua Ma, Xianghui Liu, Jia Jia, Bu-Cong Han, Ying Xue, Ze-Rong Li, Sheng-Yong Yang, Yu-Quan Wei, Yuzong Chen:
Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries. 455-467 - Hwangseo Park, Jeong-Yi Jeon, Song Yi Kim, Dae Gwin Jeong, Seong Eon Ryu:
Identification of novel inhibitors of mitogen-activated protein kinase phosphatase-1 with structure-based virtual screening. 469-475 - Sergey A. Samsonov, Joan Teyra, M. Teresa Pisabarro:
Docking glycosaminoglycans to proteins: analysis of solvent inclusion. 477-489
Volume 25, Number 6, June 2011
- Yvonne C. Martin, Terry R. Stouch:
In tribute to Corwin Hansch, father of QSAR. 491 - Cynthia Rachel Selassie:
Obituary: Corwin H. Hansch. 493-494 - Corwin Hansch:
The advent and evolution of QSAR at Pomona College. 495-507 - Toshio Fujita:
In memoriam Professor Corwin Hansch: birth pangs of QSAR before 1961. 509-517 - Yvonne C. Martin:
Remembrances of Corwin Hansch. 519-523 - Tsung-Ying Tsai, Kai-Wei Chang, Calvin Yu-Chian Chen:
iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan. 525-531 - Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Christof H. Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko:
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. 533-554 - Jakyung Yoo, José L. Medina-Franco:
Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. 555-567 - Daniel Mucs, Richard A. Bryce, Pascal Bonnet:
Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors. 569-581 - Carlos Gueto-Tettay, Juan Carlos Drosos, Ricardo Vivas-Reyes:
Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies. 583-597
Volume 25, Number 7, July 2011
- Wendy A. Warr:
Fragment-based drug discovery: what really works. An interview with Sandy Farmer of Boehringer Ingelheim. 599-605 - Chaohong Sun, Andrew M. Petros, Philip J. Hajduk:
Fragment-based lead discovery: challenges and opportunities. 607-610 - M. N. Schulz, J. Landström, K. Bright, Roderick E. Hubbard:
Design of a Fragment Library that maximally represents available chemical space. 611-620 - Wan F. Lau, Jane M. Withka, David Hepworth, Thomas V. Magee, Yuhua J. Du, Gregory A. Bakken, Michael D. Miller, Zachary S. Hendsch, Venkataraman Thanabal, Steve A. Kolodziej, Li Xing, Qiyue Hu, Lakshmi S. Narasimhan, Robert Love, Maura E. Charlton, Samantha Hughes, Willem P. van Hoorn, James E. J. Mills:
Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics. 621-636 - Lorenz C. Blum, Ruud van Deursen, Jean-Louis Reymond:
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. 637-647 - Ruud van Deursen, Lorenz C. Blum, Jean-Louis Reymond:
Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. 649-662 - Paul N. Mortenson, Christopher W. Murray:
Assessing the lipophilicity of fragments and early hits. 663-667 - Charles A. Wartchow, Frank Podlaski, Shirley Li, Karen Rowan, Xiaolei Zhang, David Mark, Kuo-Sen Huang:
Biosensor-based small molecule fragment screening with biolayer interferometry. 669-676 - Scott J. Pollack, Kim S. Beyer, Christopher Lock, Ilka Müller, David W. Sheppard, Mike Lipkin, David Hardick, Peter Blurton, Philip M. Leonard, Paul A. Hubbard, Daniel Todd, Christine M. Richardson, Thomas Ahrens, Manuel Baader, Doris Hafenbradl, Kate Hilyard, Roland W. Bürli:
A comparative study of fragment screening methods on the p38α kinase: new methods, new insights. 677-687 - M. Catherine Johnson, Qiyue Hu, Laura Lingardo, Rose Ann Ferre, Samantha Greasley, Jiangli Yan, John Kath, Ping Chen, Jacques Ermolieff, Gordon Alton:
Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery. 689-698
Volume 25, Number 8, August 2011
- Gerald M. Maggiora:
The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs? 699-708 - Jozica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura, Wilfred F. van Gunsteren:
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. 709-716 - Laura Guasch, Esther Sala, Cristina Valls, Mayte Blay, Miquel Mulero, Lluís Arola, Gerard Pujadas, Santiago Garcia-Vallvé:
Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity. 717-728 - Antonella Ciancetta, Samuel Genheden, Ulf Ryde:
A QM/MM study of the binding of RAPTA ligands to cathepsin B. 729-742 - Ivano Eberini, Simona Daniele, Chiara Parravicini, Cristina Sensi, Maria Letizia Trincavelli, Claudia Martini, Maria P. Abbracchio:
In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases. 743-752 - Brittany L. Howard, Philip E. Thompson, David T. Manallack:
Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design. 753-762 - Cátia Teixeira, José R. B. Gomes, Thierry Couesnon, Paula Gomes:
Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors. 763-775 - Paolo Tosco, Thomas Balle, Fereshteh Shiri:
Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. 777-783 - M. Stuart Armstrong, Paul W. Finn, Garrett M. Morris, W. Graham Richards:
Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension. 785-790
Volume 25, Number 9, September 2011
- Wendy A. Warr:
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University. 791-793 - Matthias Negri, Maurizio Recanatini, Rolf W. Hartmann:
Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps. 795-811 - Álvaro Cortés Cabrera, Rubén Gil-Redondo, Almudena Perona, Federico Gago, Antonio Morreale:
VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. 813-824 - Lea Toledo, Laura Masgrau, José M. Lluch, Àngels González-Lafont:
Substrate binding to mammalian 15-lipoxygenase. 825-835 - Constantinos Potamitis, Minos-Timotheos Matsoukas, Theodore V. Tselios, Thomas M. Mavromoustakos, Simona Golic Grdadolnik:
Conformational analysis of the ΜΒΡ83-99 (Phe91) and ΜΒΡ83-99 (Tyr91) peptide analogues and study of their interactions with the HLA-DR2 and human TCR receptors by using Molecular Dynamics. 837-853 - Chin Yee Liew, Yen Ching Lim, Chun Wei Yap:
Mixed learning algorithms and features ensemble in hepatotoxicity prediction. 855-871 - Dusica Vidovic, Yuli Xie, Alison Rinderspacher, Shi-Xian Deng, Donald W. Landry, Caty Chung, Deborah H. Smith, Lutz Tautz, Stephan C. Schürer:
Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype. 873-883 - Jing Lu, Mingyue Zheng, Yong Wang, Qiancheng Shen, Xiaomin Luo, Hualiang Jiang, Kaixian Chen:
Fragment-based prediction of skin sensitization using recursive partitioning. 885-893
Volume 25, Number 10, October 2011
- Andrew J. Bordner, Barry Zorman, Ruben Abagyan:
Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. 895-911 - Laurence Leherte, Daniel P. Vercauteren:
Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models. 913-930 - Tobias Lippert, Tanja Schulz-Gasch, Olivier Roche, Wolfgang Guba, Matthias Rarey:
De novo design by pharmacophore-based searches in fragment spaces. 931-945 - Feifei Tian, Yonggang Lv, Peng Zhou, Li Yang:
Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. 947-958 - Haralambos Tzoupis, Georgios Leonis, Serdar Durdagi, Varnavas D. Mouchlis, Thomas M. Mavromoustakos, Manthos G. Papadopoulos:
Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations. 959-976 - Xuefei Liu, Guoqiang Dong, Jue Zhang, Jingjing Qi, Canhui Zheng, Youjun Zhou, Ju Zhu, Chunquan Sheng, Jiaguo Lü:
Discovery of novel human acrosin inhibitors by virtual screening. 977-985 - Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Tzong-Yi Lee:
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. 987-995
Volume 25, Number 11, November 2011
- Tim Potter, Richard Lewis, Tim Luker, Roger Bonnert, Michael A. Bernstein, Timothy N. Birkinshaw, Stephen Thom, Mark Wenlock, Stuart Paine:
In silico prediction of acyl glucuronide reactivity. 997-1005 - Robert V. Swift, Rommie E. Amaro:
Modeling the pharmacodynamics of passive membrane permeability. 1007-1017 - Despina Laimou, Eliada Lazoura, Anastassios N. Troganis, Minos-Timotheos Matsoukas, Spyros N. Deraos, Maria Katsara, John Matsoukas, Vasso Apostolopoulos, Theodore V. Tselios:
Conformational studies of immunodominant myelin basic protein 1-11 analogues using NMR and molecular modeling. 1019-1032 - Orr Ravitz, Zsolt Zsoldos, Anikó Simon:
Improving molecular docking through eHiTS' tunable scoring function. 1033-1051 - Benjamin Schaefer, Caroline Kisker, Christoph A. Sotriffer:
Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design. 1053-1069 - Victor M. Anisimov, Arturas Ziemys, Smitha Kizhake, Ziyan Yuan, Amarnath Natarajan, Claudio N. Cavasotto:
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1. 1071-1084 - Samuel Genheden:
MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model. 1085-1093
Volume 25, Number 12, December 2011
- Markus Muehlbacher, Gudrun M. Spitzer, Klaus R. Liedl, Johannes Kornhuber:
Qualitative prediction of blood-brain barrier permeability on a large and refined dataset. 1095-1106 - Aldo Segura-Cabrera, Virgilio Bocanegra-García, Cristian Lizarazo-Ortega, Xianwu Guo, José Correa-Basurto, Mario A. Rodríguez-Pérez:
A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design. 1107-1119 - Ozgur Demir-Kavuk, Jörg Bentzien, Ingo Muegge, Ernst-Walter Knapp:
DemQSAR: predicting human volume of distribution and clearance of drugs. 1121-1133 - P. García-Gutiérrez, A. Landa-Piedra, Adela Rodríguez-Romero, R. Parra-Unda, Arturo Rojo-Domínguez:
Novel inhibitors to Taenia solium Cu/Zn superoxide dismutase identified by virtual screening. 1135-1145 - Natalja Fjodorova, Marjana Novic, Alessandra Roncaglioni, Emilio Benfenati:
Evaluating the applicability domain in the case of classification predictive models for carcinogenicity based on the counter propagation artificial neural network. 1147-1158 - Natalja Fjodorova, Marjana Novic:
Some findings relevant to the mechanistic interpretation in the case of predictive models for carcinogenicity based on the counter propagation artificial neural network. 1159-1169 - Calvin Santiago, Kong T. Nguyen, Matthieu Schapira:
Druggability of methyl-lysine binding sites. 1171-1178
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