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ORCIDJournal of Computer-Aided Molecular Design, Volume 30
Volume 30, Number 1, January 2016
- Mengjun Wu, Martin Vogt, Gerald M. Maggiora
, Jürgen Bajorath:
Design of chemical space networks on the basis of Tversky similarity. 1-12 - Justyna Bednarko, Justyna Wielinska, Karol Sikora, Beata Liberek, Andrzej Nowacki:
Theoretical studies on the reaction of mono- and ditriflate derivatives of 1, 4: 3, 6-dianhydro-d-mannitol with trimethylamine - Can a quaternary ammonium salt be a source of the methyl group? 13-26 - Hua-Jun Luo, Jun-Zhi Wang, Nian-Yu Huang, Wei-Qiao Deng, Kun Zou:
Computational insights into the interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives with H+, K+-ATPase at different pH. 27-37 - Rand Shahin, Lubna Swellmeen, Omar Shaheen, Nour Aboalhaija, Maha Habash:
Identification of novel inhibitors for Pim-1 kinase using pharmacophore modeling based on a novel method for selecting pharmacophore generation subsets. 39-68 - Raoni Almeida de Souza, Natalia Díaz, Ronaldo Alves Pinto Nagem, Rafaela Salgado Ferreira, Dimas Suárez:
Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations. 69-83 - Cecylia S. Lupala, Patricia Gómez-Gutiérrez, Juan Jesús Pérez:
New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding. 85-101
Volume 30, Number 2, February 2016
- Anthony Nicholls:
Confidence limits, error bars and method comparison in molecular modeling. Part 2: comparing methods. 103-126 - Ann E. Cleves, Ajay N. Jain:
Extrapolative prediction using physically-based QSAR. 127-152 - Nikolaos N. Louros, Fotis A. Baltoumas, Stavros J. Hamodrakas, Vassiliki A. Iconomidou:
A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. 153-164 - Anna Rybinska, Anita Sosnowska, Maciej Barycki, Tomasz Puzyn:
Geometry optimization method versus predictive ability in QSPR modeling for ionic liquids. 165-176 - Jeffrey L. Mendenhall, Jens Meiler:
Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout. 177-189
Volume 30, Number 3, March 2016
- Martin Vogt, Dagmar Stumpfe, Gerald M. Maggiora, Jürgen Bajorath:
Lessons learned from the design of chemical space networks and opportunities for new applications. 191-208 - Gregory Sliwoski, Jeffrey L. Mendenhall, Jens Meiler:
Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. 209-217 - Zhiqiang Yan, Jin Wang:
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks. 219-227 - Swapnil Chavan, Ahmed Abdelaziz, Jesper G. Wiklander, Ian A. Nicholls:
A k-nearest neighbor classification of hERG K+ channel blockers. 229-236 - Mohammad Mahdi Jaghoori, Boris Bleijlevens, Sílvia Delgado Olabarriaga:
1001 Ways to run AutoDock Vina for virtual screening. 237-249 - Erika Piccirillo, Benjamin Merget, Christoph A. Sotriffer, Antonia T. do Amaral:
Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence. 251-270 - Sam Lear, Steven L. Cobb:
Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment. 271-277
Volume 30, Number 4, April 2016
- Anthony Nicholls:
Statistics in molecular modeling: a summary. 279-280 - Wendy A. Warr:
MOOCers and shakers and chemistry course takers. 281-284 - Eleonora Gianti, Troy E. Messick, Paul M. Lieberman, Randy J. Zauhar:
Computational analysis of EBNA1 "druggability" suggests novel insights for Epstein-Barr virus inhibitor design. 285-303 - Lucas N. Alberca, María L. Sbaraglini, Darío E. Balcazar, Laura Fraccaroli, Carolina Carrillo, Andrea Medeiros, Diego Benitez, Marcelo A. Comini, Alan Talevi:
Discovery of novel polyamine analogs with anti-protozoal activity by computer guided drug repositioning. 305-321 - Takako Takeda, Yanli Wang, Stephen H. Bryant:
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold. 323-330 - Jon G. Wilkes, Iva B. Stoyanova-Slavova, Dan A. Buzatu:
Alignment-independent technique for 3D QSAR analysis. 331-345 - Sehan Lee, Mace G. Barron:
A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs. 347-363
Volume 30, Number 5, May 2016
- María Garrido-Arandia, Jorge Bretones, Cristina Gómez-Casado, Nuria Cubells, Araceli Díaz-Perales, Luis Fernández Pacios:
Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold. 365-379 - Jaroslaw Polanski, Jacek Bogocz, Aleksandra Tkocz:
The analysis of the market success of FDA approvals by probing top 100 bestselling drugs. 381-389 - Johannes R. Loeffler, Emanuel S. R. Ehmki, Julian E. Fuchs, Klaus R. Liedl:
Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. 391-400 - Shweta Kulshreshtha, Vigi Chaudhary, Girish K. Goswami, Nidhi Mathur:
Computational approaches for predicting mutant protein stability. 401-412 - Zhi-Jiang Yao, Jie Dong, Yu-Jing Che, Min-Feng Zhu, Ming Wen, Ning-Ning Wang, Shan Wang, Aiping Lu, Dong-Sheng Cao:
TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. 413-424 - Tomoyuki Miyao, Hiromasa Kaneko, Kimito Funatsu:
Ring system-based chemical graph generation for de novo molecular design. 425-446
Volume 30, Number 6, June 2016
- Andrew Anighoro, Jürgen Bajorath:
Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor. 447-456 - Ashutosh Kumar, Kam Y. J. Zhang:
A pose prediction approach based on ligand 3D shape similarity. 457-469 - Patcharapong Thangsunan, Sila Kittiwachana, Puttinan Meepowpan, Nawee Kungwan, Panchika Prangkio, Supa Hannongbua, Nuttee Suree:
Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches. 471-488 - Fotis A. Baltoumas, Margarita C. Theodoropoulou, Stavros J. Hamodrakas:
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. 489-512 - Antonio Cardone, Mary Brady, Ram D. Sriram, Harish C. Pant, Sergio A. Hassan:
Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore. 513-521
Volume 30, Number 7, July 2016
- Ryo Kunimoto, Martin Vogt, Jürgen Bajorath:
Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure. 523-531 - Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo:
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. 533-539 - Rodrigo Ochoa, Stanley J. Watowich, Andrés F. Flórez, Carol V. Mesa, Sara M. Robledo, Carlos Muskus:
Drug search for leishmaniasis: a virtual screening approach by grid computing. 541-552 - Juan Li, Huisheng Fang:
A comparison of different functions for predicted protein model quality assessment. 553-558 - Alexey V. Rossokhin, Boris S. Zhorov:
Side chain flexibility and the pore dimensions in the GABAA receptor. 559-567 - Onur Serçinoglu, Gülin Özcan, Zeynep Kutlu Kabas, Pemra Ozbek:
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis. 569-581
Volume 30, Number 8, August 2016
- Mathias M. von Behren, Stefan Bietz, Eva Nittinger, Matthias Rarey:
mRAISE: an alternative algorithmic approach to ligand-based virtual screening. 583-594 - Steven Kearnes, Kevin McCloskey, Marc Berndl, Vijay S. Pande, Patrick Riley:
Molecular graph convolutions: moving beyond fingerprints. 595-608 - Steven Kearnes, Vijay S. Pande:
ROCS-derived features for virtual screening. 609-617 - Agustina Arroyuelo, Jorge A. Vila, Osvaldo A. Martin:
Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules. 619-624 - Nam-Chul Cho, Seoung-Hwan Seo, Dohee Kim, Ji-Sun Shin, Jeongmin Ju, Jihye Seong, Seon Hee Seo, Iiyoun Lee, Kyung-Tae Lee, Yun Kyung Kim, Kyoung Tai No, Ae Nim Pae:
Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist. 625-637 - Nguyen Quoc Thai, Ning-Hsuan Tseng, Mui Thi Vu, Tin Trung Nguyen, Huynh Quang Linh, Chin-Kun Hu, Yun-Ru Chen, Mai Suan Li:
Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study. 639-650
Volume 30, Number 9, September 2016
- Symon Gathiaka, Shuai Liu, Michael Chiu, Huanwang Yang, Jeanne A. Stuckey, You-Na Kang, Jim Delproposto, Ginger Kubish, James B. Dunbar Jr., Heather A. Carlson, Stephen K. Burley, W. Patrick Walters, Rommie E. Amaro, Victoria A. Feher, Michael K. Gilson:
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. 651-668 - Inna Slynko, Franck Da Silva, Guillaume Bret, Didier Rognan:
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. 669-683 - Ashutosh Kumar, Kam Y. J. Zhang:
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015. 685-693 - Zhaofeng Ye, Matthew P. Baumgartner, Bentley M. Wingert, Carlos J. Camacho:
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge. 695-706 - Majda Misini Ignjatovic, Octav Caldararu, Geng Dong, Camila Muñoz-Gutiérrez, Francisco Adasme-Carreño, Ulf Ryde:
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations. 707-730 - Diogo Santos-Martins:
Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015. 731-742 - Nan-Jie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy:
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. 743-751 - Stefano Piotto, Luigi Di Biasi, Riccardo Fino, Raffaele Parisi, Lucia Sessa, Simona Concilio:
Yada: a novel tool for molecular docking calculations. 753-759 - Jocelyn Sunseri, Matthew Ragoza, Jasmine Collins, David Ryan Koes:
A D3R prospective evaluation of machine learning for protein-ligand scoring. 761-771 - Veronica Salmaso, Mattia Sturlese, Alberto Cuzzolin, Stefano Moro:
DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015. 773-789 - Sergei Grudinin, Maria Kadukova, Andreas Eisenbarth, Simon Marillet, Frédéric Cazals:
Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation. 791-804 - Sergio Ruiz-Carmona, Xavier Barril:
Docking-undocking combination applied to the D3R Grand Challenge 2015. 805-815 - Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi:
Improved pose and affinity predictions using different protocols tailored on the basis of data availability. 817-828 - Edithe Selwa, Virginie Y. Martiny, Bogdan I. Iorga:
Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets. 829-839
Volume 30, Number 10, October 2016
- Andrew Anighoro, Antonio de la Vega de León, Jürgen Bajorath:
Predicting bioactive conformations and binding modes of macrocycles. 841-849 - Jacopo Sgrignani, Filomena De Luca, Hayarpi Torosyan, Jean-Denis Docquier, Da Duan, Beatrice Novati, Fabio Prati, Giorgio Colombo, Giovanni Grazioso:
Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors. 851-861 - Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman:
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. 863-874 - Takeshi Ishikawa:
Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation. 875-887 - Hui Zhang, Lan Ding, Yi Zou, Shui-Qing Hu, Hai-Guo Huang, Wei-Bao Kong, Ji Zhang:
Predicting drug-induced liver injury in human with Naïve Bayes classifier approach. 889-898 - Bipin Singh, Gopalakrishnan Bulusu, Abhijit Mitra:
Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity. 899-916 - Jiraphorn Phanich, Thanyada Rungrotmongkol, Nawee Kungwan, Supot Hannongbua:
Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. 917-926
Volume 30, Number 11, November 2016
- Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley:
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. 927-944 - Ariën S. Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A. Feng, Daniel F. Ortwine, David L. Mobley, John D. Chodera:
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. 945-958 - Andreas Klamt, Frank Eckert, Jens Reinisch, Karin Wichmann:
Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set. 959-967 - Samuel Genheden, Jonathan W. Essex:
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. 969-976 - Ganesh Kamath, Igor Kurnikov, Boris Fain, Igor V. Leontyev, Alexey A. Illarionov, Oleg Butin, Michael A. Olevanov, Leonid B. Pereyaslavets:
Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields. 977-988 - Gerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael R. Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks:
Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge. 989-1006 - Sebastian Diaz-Rodriguez, Samantha M. Bozada, Jeremy R. Phifer, Andrew S. Paluch:
Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model. 1007-1017 - Kee-Choo Chung, Hwangseo Park:
Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules. 1019-1033 - Nicolas Tielker, Daniel Tomazic, Jochen Heil, Thomas Kloss, Sebastian Ehrhart, Stefan Güssregen, K. Friedemann Schmidt, Stefan M. Kast:
The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D. 1035-1044 - Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga:
Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. 1045-1058 - S. Shanaka Paranahewage, Cassidy S. Gierhart, Christopher J. Fennell:
Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields. 1059-1065 - Emiliano Brini, S. Shanaka Paranahewage, Christopher J. Fennell, Ken A. Dill:
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. 1067-1077 - Diogo Santos-Martins, Pedro Alexandrino Fernandes, Maria João Ramos:
Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. 1079-1086 - Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks:
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. 1087-1100 - Stefano Bosisio, Antonia S. J. S. Mey, Julien Michel:
Blinded predictions of distribution coefficients in the SAMPL5 challenge. 1101-1114 - Tyler Luchko, Nikolay Blinov, Garrett C. Limon, Kevin P. Joyce, Andriy Kovalenko:
SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling. 1115-1127 - Michael R. Jones, Bernard R. Brooks, Angela K. Wilson:
Partition coefficients for the SAMPL5 challenge using transfer free energies. 1129-1138
Volume 30, Number 12, December 2016
- Bradley Sherborne, Veerabahu Shanmugasundaram, Alan C. Cheng, Clara D. Christ, Renee L. DesJarlais, José S. Duca, Richard A. Lewis, Deborah A. Loughney, Eric S. Manas, Georgia B. McGaughey, Catherine E. Peishoff, Herman van Vlijmen:
Collaborating to improve the use of free-energy and other quantitative methods in drug discovery. 1139-1141 - Wendy A. Warr:
Blowing a breath of fresh share on data. 1143-1147 - Mámon M. Hatmal, Shadi Jaber, Mutasem O. Taha:
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies. 1149-1163 - Hugo de Almeida, Vincent Leroux, Flávia Nader Motta, Philippe Grellier, Bernard Maigret, Jaime Martins Santana, Izabela Marques Dourado Bastos:
Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening. 1165-1174 - Remigijus Didziapetris, Kiril Lanevskij:
Compilation and physicochemical classification analysis of a diverse hERG inhibition database. 1175-1188 - Hongli Liu, Rui Han, Jiazhong Li, Huanxiang Liu, Lifang Zheng:
Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation. 1189-1200
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