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ORCIDJournal of Computer-Aided Molecular Design, Volume 27
Volume 27, Number 1, January 2013
- Peter W. Kenny, Carlos Alberto Montanari
:
Inflation of correlation in the pursuit of drug-likeness. 1-13 - Nadine Schneider, Gudrun Lange, Sally A. Hindle, Robert Klein, Matthias Rarey:
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. 15-29 - David Zanuy, Francisco J. Sayago, Guillem Revilla-López, Gema Ballano, Lilach Agemy, Venkata Ramana Kotamraju, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, April M. Sawvel, Galen Stucky, Erkki Ruoslahti, Carlos Alemán:
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing. 31-43 - Adam Jarmula, Wojciech Rode:
Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase. 45-66 - Peng Zhou, Congcong Wang, Feifei Tian, Yanrong Ren, Chao Yang, Jian Huang:
Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity. 67-78 - Ma José Jerez, Miguel Jerez, Coral González-García, Sara Ballester, Ana Castro:
Combined use of pharmacophoric models together with drug metabolism and genotoxicity "in silico" studies in the hit finding process. 79-90 - Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng:
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. 91-103 - Pavel V. Klimovich, David L. Mobley:
Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. 105
Volume 27, Number 2, February 2013
- Garland R. Marshall:
Limiting assumptions in molecular modeling: electrostatics. 107-114 - Ye Hu, Gerald M. Maggiora, Jürgen Bajorath:
Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. 115-124 - Zoya Titarenko, Natalya Vasilevich, Vladimir Zernov, Michael Kirpichenok, Dmitry Genis:
Oxygen-containing fragments in natural products. 125-160 - Ishrat Jabeen, Penpun Wetwitayaklung, Peter Chiba, Manuel Pastor, Gerhard F. Ecker:
2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3, 4b][1, 4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein. 161-171 - Biprashekhar Chakraborty, Raisa Mukherjee, Jayati Sengupta:
Structural insights into the mechanism of translational inhibition by the fungicide sordarin. 173-184 - Bernardo Palacios-Bejarano, Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
QSAR model based on weighted MCS trees approach for the representation of molecule data sets. 185-201
Volume 27, Number 3, March 2013
- David J. Wood, Lars Carlsson, Martin Eklund, Ulf Norinder, Jonna C. Stålring:
QSAR with experimental and predictive distributions: an information theoretic approach for assessing model quality. 203-219 - G. Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman:
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. 221-234 - Meekyum Olivia Kim, Sara E. Nichols, Yi Wang, James Andrew McCammon:
Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. 235-246 - Kongkai Zhu, Junyan Lu, Zhongjie Liang, Xiangqian Kong, Fei Ye, Lu Jin, Heji Geng, Yong Chen, Mingyue Zheng, Hualiang Jiang, Jun-Qian Li, Cheng Luo:
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. 247-256 - Nabanita Saikia, Sanchaita Rajkhowa, Ramesh C. Deka:
Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein. 257-276 - Marcus Malo, Ronnie Persson, Peder Svensson, Kristina Luthman, Lars Brive:
Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor. 277-291 - Dmitry Lupyan, Yuriy A. Abramov, Woody Sherman:
Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. 293
Volume 27, Number 4, April 2013
- Michael M. H. Graf, Urban Bren, Dietmar Haltrich, Chris Oostenbrink:
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. 295-304 - Tony Ngo, Timothy J. Nicholas, Junli Chen, Angela M. Finch, Renate Griffith:
5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists. 305-319 - Richard Cox, Darren V. S. Green, Christopher N. Luscombe, Noj Malcolm, Stephen D. Pickett:
QSAR workbench: automating QSAR modeling to drive compound design. 321-336 - Reem Al Olaby, Hassan M. Azzazy, Rodney Harris, Brett Chromy, Jost Vielmetter, Rod Balhorn:
Identification of ligands that target the HCV-E2 binding site on CD81. 337-346 - Rameshwar Prajapati, Udghosh Singh, Abhijeet Patil, Kailas S. Khomane, Pravin Bagul, Arvind K. Bansal, Abhay T. Sangamwar:
In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies. 347-363 - Hao Wang, Richard B. Sessions, Stephen S. Prime, Deborah K. Shoemark, Shelley J. Allen, Wei Hong, Sathya Narayanan, Ian C. Paterson:
Identification of novel small molecule TGF-β antagonists using structure-based drug design. 365-372 - Kamil Malác, Ivan Barvík:
Substrate recognition by norovirus polymerase: microsecond molecular dynamics study. 373-388
Volume 27, Number 5, May 2013
- Peter W. Kenny, Carlos Alberto Montanari, Igor M. Prokopczyk:
ClogPalk: a method for predicting alkane/water partition coefficient. 389-402 - José L. Domínguez, M. Carmen Villaverde, Fredy Sussman:
Effect of pH and ligand charge state on BACE-1 fragment docking performance. 403-417 - Teppei Ebina, Yuki Umezawa, Yutaka Kuroda:
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. 419-426 - Igor I. Baskin, Nelly I. Zhokhova:
The continuous molecular fields approach to building 3D-QSAR models. 427-442 - Yufeng Jane Tseng, Eric J. Martin, Cristian Bologa, Anang A. Shelat:
Cheminformatics aspects of high throughput screening: from robots to models: symposium summary. 443-453 - Carol A. Mulrooney, David L. Lahr, Michael J. Quintin, Willmen Youngsaye, Dennis Moccia, Jacob K. Asiedu, Evan L. Mulligan, Lakshmi B. Akella, Lisa A. Marcaurelle, Philip Montgomery, Joshua A. Bittker, Paul A. Clemons, Steve Brudz, Sivaraman Dandapani, Jeremy R. Duvall, Nicola J. Tolliday, Andrea de Souza:
An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries. 455-468 - Michael R. Browning, Bradley T. Calhoun, Sanjay Joshua Swamidass:
Managing missing measurements in small-molecule screens. 469-478
Volume 27, Number 6, June 2013
- Takeshi Ashida, Takeshi Kikuchi:
Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system. 479-490 - Marta Del Cadia, Francesca De Rienzo, Maria Cristina Menziani:
Approaching the 5-HT3 receptor heterogeneity by computational studies of the transmembrane and intracellular domains. 491-509 - Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer:
Protein pocket and ligand shape comparison and its application in virtual screening. 511-524 - Jan Jakubik, Alena Randáková, Vladimír Dolezal:
On homology modeling of the M2 muscarinic acetylcholine receptor subtype. 525-538 - Wenshuai Zhang, Xiaoyan Zeng, Li Zhang, Haiyan Peng, Yongjun Jiao, Jun Zeng, Herbert R. Treutlein:
Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5). 539-550 - Michal Brylinski, Wei Pan Feinstein:
eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. 551-567
Volume 27, Number 7, July 2013
- Miriam Gochin, Landon R. Whitby, Aaron H. Phillips, Dale L. Boger:
NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41. 569-582 - Villu Ruusmann, Uko Maran:
From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions. 583-603 - Mahmoud Kandeel, Yukio Kitade:
In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference. 605-614 - Rafik Karaman, Hiba Ghareeb, Khuloud Kamal Dajani, Laura Scrano, Hussein Hallak, Saleh Abu-Lafi, Gennaro Mecca, Sabino A. Bufo:
Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions. 615-635 - Utsab Debnath, Saroj Verma, Surabhi Jain, Setu B. Katti, Yenamandra S. Prabhakar:
Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics. 637-654
Volume 27, Number 8, August 2013
- Peter W. Kenny, Carlos Alberto Montanari, Igor M. Prokopczyk, Fernanda A. Sala, Geraldo Rodrigues Sartori:
Automated molecule editing in molecular design. 655-664 - Disha Gupta-Ostermann, Ye Hu, Jürgen Bajorath:
Systematic mining of analog series with related core structures in multi-target activity space. 665-674 - Pavel G. Polishchuk, Timur I. Madzhidov, Alexandre Varnek:
Estimation of the size of drug-like chemical space based on GDB-17 data. 675-679 - Sedat Karabulut, Hilmi Namli, Jerzy Leszczynski:
Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint. 681-688 - Diem-Trang T. Tran, Ly Le, Thanh N. Truong:
Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase. 689-695 - Chunli Pang, Tianguang Cao, Junwei Li, Mengwen Jia, Suhua Zhang, Shuxi Ren, Hailong An, Yong Zhan:
Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs. 697-705 - James S. Wright, James M. Anderson, Hooman Shadnia, Tony Durst, John A. Katzenellenbogen:
Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation. 707-721 - Andrej Perdih, Gerhard Wolber, Tomaz Solmajer:
Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase. 723-738 - David Fernández, Joaquín Ortega-Castro, Juan Frau:
Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study. 739-754
Volume 27, Number 9, September 2013
- Shuai Liu, Yujie Wu, Teng Lin, Robert Abel, Jonathan P. Redmann, Christopher M. Summa, Vivian R. Jaber, Nathan M. Lim, David L. Mobley:
Lead optimization mapper: automating free energy calculations for lead optimization. 755-770 - Derek A. Debe, Ravindra B. Mamidipaka, Robert J. Gregg, James T. Metz, Rishi R. Gupta, Steven W. Muchmore:
ALOHA: a novel probability fusion approach for scoring multi-parameter drug-likeness during the lead optimization stage of drug discovery. 771-782 - Shahul H. Nilar, Ngai Ling Ma, Thomas H. Keller:
The importance of molecular complexity in the design of screening libraries. 783-792 - Elena Salmina, Maria A. Grishina, Vladimir Potemkin:
An approximation of the Cioslowski-Mixon bond order indexes using the AlteQ approach. 793-805 - Nabanita Saikia, Ramesh C. Deka:
Ab initio study on the noncovalent adsorption of camptothecin anticancer drug onto graphene, defect modified graphene and graphene oxide. 807-821 - Bianca Pérez, Sandra Antunes, Lídia M. Gonçalves, Ana Domingos, José R. B. Gomes, Paula Gomes, Cátia Teixeira:
Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies. 823-835
Volume 27, Number 10, October 2013
- Gergely Tóth, Zsolt Bodai, Károly Héberger:
Estimation of influential points in any data set from coefficient of determination and its leave-one-out cross-validated counterpart. 837-844 - Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones:
Computational analysis of local membrane properties. 845-858 - Grace Mugumbate, Ana S. Newton, Philip J. Rosenthal, Jiri Gut, Rui Moreira, Kelly Chibale, Rita C. Guedes:
Novel anti-Plasmodial hits identified by virtual screening of the ZINC database. 859-871 - Jose C. Jimenez-Lopez, Simeon O. Kotchoni, Maria C. Hernandez-Soriano, Emma W. Gachomo, Juan D. Alché:
Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen. 873-895 - Haoliang Yuan, Wenting Tai, Shihe Hu, Haichun Liu, Yanmin Zhang, Sihui Yao, Ting Ran, Shuai Lu, Zhipeng Ke, Xiao Xiong, Jinxing Xu, Yadong Chen, Tao Lu:
Fragment-based strategy for structural optimization in combination with 3D-QSAR. 897-915
Volume 27, Number 11, November 2013
- Rocco Varela, Ann E. Cleves, Russell Spitzer, Ajay N. Jain:
A structure-guided approach for protein pocket modeling and affinity prediction. 917-934 - Zhiwei Yang, Gang Yang, Lijun Zhou:
Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. 935-950 - El Hassane Anouar, Salwa Raweh, Imene Bayach, Muhammad Taha, Mohd Syukri Baharudin, Florent Di Meo, Mizaton Hazizul Hasan, Aishah Adam, Nor Hadiani Ismail, Jean-Frédéric F. Weber, Patrick Trouillas:
Antioxidant properties of phenolic Schiff bases: structure-activity relationship and mechanism of action. 951-964 - Jianzhong Chen, Jinan Wang, Weiliang Zhu, Guohui Li:
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. 965-974 - Clelia Dallanoce, Giovanni Grazioso, Diego Yuri Pomè, Miriam Sciaccaluga, Carlo Matera, Cecilia Gotti, Sergio Fucile, Marco De Amici:
Investigating the hydrogen-bond acceptor site of the nicotinic pharmacophore model: a computational and experimental study using epibatidine-related molecular probes. 975-987
Volume 27, Number 12, December 2013
- Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts:
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. 989-1007 - Randy J. Zauhar, Eleonora Gianti, William J. Welsh:
Fragment-based Shape Signatures: a new tool for virtual screening and drug discovery. 1009-1036 - Malgorzata N. Drwal, Keli Agama, Yves Pommier, Renate Griffith:
Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket. 1037-1049 - Joseph J. Crivelli, Gordon Lemmon, Kristian Kaufmann, Jens Meiler:
Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. 1051-1065 - Wen Tan, Hu Mei, Li Chao, Tengfei Liu, Xianchao Pan, Mao Shu, Li Yang:
Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors. 1067-1073 - Sawsan Abuhamdah, Maha Habash, Mutasem O. Taha:
Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors. 1075-1092
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