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Journal 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
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing. 31-43 - Adam Jarmula
Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase. 45-66 - Peng Zhou
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
Combined use of pharmacophoric models together with drug metabolism and genotoxicity "in silico" studies in the hit finding process. 79-90 - Tzu-Hao Chang
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
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
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
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
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
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. 247-256 - Nabanita Saikia
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
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
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. 295-304 - Tony Ngo
5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists. 305-319 - Richard Cox, Darren V. S. Green
QSAR workbench: automating QSAR modeling to drive compound design. 321-336 - Reem Al Olaby, Hassan M. Azzazy
Identification of ligands that target the HCV-E2 binding site on CD81. 337-346 - Rameshwar Prajapati, Udghosh Singh, Abhijeet Patil, Kailas S. Khomane
In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies. 347-363 - Hao Wang
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
ClogPalk: a method for predicting alkane/water partition coefficient. 389-402 - José L. Domínguez, M. Carmen Villaverde
Effect of pH and ligand charge state on BACE-1 fragment docking performance. 403-417 - Teppei Ebina
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. 419-426 - Igor I. Baskin
The continuous molecular fields approach to building 3D-QSAR models. 427-442 - Yufeng Jane Tseng
Cheminformatics aspects of high throughput screening: from robots to models: symposium summary. 443-453 - Carol A. Mulrooney, David L. Lahr
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
Protein pocket and ligand shape comparison and its application in virtual screening. 511-524 - Jan Jakubik
On homology modeling of the M2 muscarinic acetylcholine receptor subtype. 525-538 - Wenshuai Zhang, Xiaoyan Zeng, Li Zhang, Haiyan Peng, Yongjun Jiao, Jun Zeng
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
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
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
Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions. 615-635 - Utsab Debnath, Saroj Verma
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
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
Estimation of the size of drug-like chemical space based on GDB-17 data. 675-679 - Sedat Karabulut
Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint. 681-688 - Diem-Trang T. Tran
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
Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase. 723-738 - David Fernández, Joaquín Ortega-Castro
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
An approximation of the Cioslowski-Mixon bond order indexes using the AlteQ approach. 793-805 - Nabanita Saikia
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
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
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
Novel anti-Plasmodial hits identified by virtual screening of the ZINC database. 859-871 - Jose C. Jimenez-Lopez
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
Fragment-based strategy for structural optimization in combination with 3D-QSAR. 897-915
Volume 27, Number 11, November 2013
- Rocco Varela, Ann E. Cleves
A structure-guided approach for protein pocket modeling and affinity prediction. 917-934 - Zhiwei Yang
Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. 935-950 - El Hassane Anouar
Antioxidant properties of phenolic Schiff bases: structure-activity relationship and mechanism of action. 951-964 - Jianzhong Chen
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. 965-974 - Clelia Dallanoce
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
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. 989-1007 - Randy J. Zauhar, Eleonora Gianti
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
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
Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors. 1075-1092
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