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ORCIDJournal of Computer-Aided Molecular Design, Volume 33
Volume 33, Number 1, January 2019
- Zied Gaieb, Conor D. Parks, Michael Chiu
, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Millard H. Lambert, Neysa Nevins, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson:
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. 1-18 - Jocelyn Sunseri, Jonathan E. King, Paul G. Francoeur, David Ryan Koes:
Convolutional neural network scoring and minimization in the D3R 2017 community challenge. 19-34 - Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov:
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. 35-46 - Ashutosh Kumar, Kam Y. J. Zhang:
Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. 47-59 - Bing Xie, David D. L. Minh:
Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 - Binding free energies between flexible ligands and rigid receptors. 61-69 - Duc Duy Nguyen, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Cao, Guo-Wei Wei:
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges. 71-82 - Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin:
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. 83-91 - Ludovic Chaput, Edithe Selwa, Eddy Elisée, Bogdan I. Iorga:
Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations. 93-103 - Xibing He, Viet Hoang Man, Beihong Ji, Xiang-Qun Xie, Junmei Wang:
Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. 105-117 - Mikhail Ignatov, Cong Liu, Andrey Alekseenko, Zhuyezi Sun, Dzmitry Padhorny, Sergei Kotelnikov, Andrey M. Kazennov, Ivan Grebenkin, Yaroslav Kholodov, Istvan Kolosvari, Alberto Pérez, Ken A. Dill, Dima Kozakov:
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. 119-127
Volume 33, Number 2, February 2019
- Terry Richard Stouch:
The backbone of our chemical computations. 129-131 - Pnina Dauber-Osguthorpe, Arnold T. Hagler:
Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? 133-203 - Arnold T. Hagler:
Force field development phase II: Relaxation of physics-based criteria... or inclusion of more rigorous physics into the representation of molecular energetics. 205-264 - Kostas A. Triantaphyllopoulos, Fotis A. Baltoumas, Stavros J. Hamodrakas:
Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). 265-285 - Lucia Fusani, Álvaro Cortés Cabrera:
Active learning strategies with COMBINE analysis: new tricks for an old dog. 287-294 - Francesca Spyrakis, Pierangelo Bellio, Antonio Quotadamo, Pasquale Linciano, Paolo Benedetti, Giulia D'Arrigo, Massimo Baroni, Laura Cendron, Giuseppe Celenza, Donatella Tondi:
First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase. 295-305
Volume 33, Number 3, March 2019
- Eva Nittinger, Paul Gibbons, Charles Eigenbrot, Doug R. Davies, Brigitte Maurer, Christine L. Yu, James R. Kiefer, Andreas Kuglstatter, Jeremy Murray, Daniel F. Ortwine, Yong Tang, Vickie Tsui:
Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison. 307-330 - Arkadii I. Lin, Dragos Horvath, Gilles Marcou, Bernd Beck, Alexandre Varnek:
Multi-task generative topographic mapping in virtual screening. 331-343 - Kai Liu, Hironori Kokubo:
Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations. 345-356 - Vagolu Siva Krishna, Shan Zheng, Estharla Madhu Rekha, Luke W. Guddat, Dharmarajan Sriram:
Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors as therapeutic drug leads. 357-366 - Xianjin Xu, Zhiwei Ma, Rui Duan, Xiaoqin Zou:
Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight. 367-374 - Jia Xin Soong, Soo Khim Chan, Theam Soon Lim, Yee-Siew Choong:
Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3). 375-385
Volume 33, Number 4, April 2019
- Pagadala Nataraj Sekhar:
AZT acts as an anti-influenza nucleotide triphosphate targeting the catalytic site of A/PR/8/34/H1N1 RNA dependent RNA polymerase. 387-404 - Xin Hu, Ya-Qin Zhang, Olivia W. Lee, Li Liu, Manshu Tang, Kent Lai, Matthew B. Boxer, Matthew D. Hall, Min Shen:
Discovery of novel inhibitors of human galactokinase by virtual screening. 405-417 - P. Chellapandi, R. Prathiviraj, A. Prisilla:
Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints. 419-436 - Han Chen, Yan Wang, Zheng Gao, Wen Yang, Jian Gao:
Assessing the performance of three resveratrol in binding with SIRT1 by molecular dynamics simulation and MM/GBSA methods: the weakest binding of resveratrol 3 to SIRT1 triggers a possibility of dissociation from its binding site. 437-446 - Haixia Ge, Yuemin Bian, Xibing He, Xiang-Qun Xie, Junmei Wang:
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. 447-459
Volume 33, Number 5, May 2019
- Saad Raza, Kara E. Ranaghan, Marc van der Kamp, Christopher J. Woods, Adrian J. Mulholland, Syed Sikander Azam:
Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site. 461-475 - Oanh Vu, Jeffrey L. Mendenhall, Doaa Altarawy, Jens Meiler:
BCL: : Mol2D - a robust atom environment descriptor for QSAR modeling and lead optimization. 477-486 - Mei Qian Yau, Abigail L. Emtage, Nathaniel J. Y. Chan, Stephen W. Doughty, Jason S. E. Loo:
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures. 487-496 - Satoshi Yamasaki, Takayuki Amemiya, Yukimitsu Yabuki, Katsuhisa Horimoto, Kazuhiko Fukui:
ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow. 497-507 - Omar Kana, Michal Brylinski:
Elucidating the druggability of the human proteome with eFindSite. 509-519 - Cheng-Shi Jiang, Yong-Xi Ge, Zhi-Qiang Cheng, Jia-Li Song, Yin-Yin Wang, Kongkai Zhu, Hua Zhang:
Discovery of new multifunctional selective acetylcholinesterase inhibitors: structure-based virtual screening and biological evaluation. 521-530
Volume 33, Number 6, June 2019
- Ajay N. Jain, Ann E. Cleves, Qi Gao, Xiao Wang, Yizhou Liu, Edward C. Sherer, Mikhail Y. Reibarkh:
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. 531-558 - Filip Miljkovic, Martin Vogt, Jürgen Bajorath:
Systematic computational identification of promiscuity cliff pathways formed by inhibitors of the human kinome. 559-572 - Lee H. Wink, Daniel L. Baker, Judith A. Cole, Abby L. Parrill:
A benchmark study of loop modeling methods applied to G protein-coupled receptors. 573-595 - Josephine Alba, Edoardo Milanetti, Marco D'Abramo:
On the activation and deactivation pathways of the Lck kinase domain: a computational study. 597-603 - Vijaya Kumar Hinge, Dipankar Roy, Andriy Kovalenko:
Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds. 605-611
Volume 33, Number 7, July 2019
- Daniel Soler, Yvonne Westermaier, Robert Soliva:
Extensive benchmark of rDock as a peptide-protein docking tool. 613-626 - Pedro A. Sánchez-Murcia, Alberto Mills, Álvaro Cortés Cabrera, Federico Gago:
Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. 627-644 - Farman Ali, Saeed Ahmed, Zar Nawab Khan Swati, Shahid Akbar:
DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information. 645-658 - Guangpu Liu, Yang Jiao, Chunxi Huang, Ping Chang:
Identification of novel and potent small-molecule inhibitors of tubulin with antitumor activities by virtual screening and biological evaluations. 659-664 - Irena Roterman, Dawid Dulak, Malgorzata Gadzala, Mateusz Banach, Leszek Konieczny:
Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution. 665-675 - Asima Hameed, Sara Masood, Aamir Hameed, Ejaz Ahmed, Ahsan Sharif, Muhammad Imran Abdullah:
Anti-malarial, cytotoxicity and molecular docking studies of quinolinyl chalcones as potential anti-malarial agent. 677-688 - Min Han, Dongdong Sun:
Rational creation and systematic analysis of cervical cancer kinase-inhibitor binding profile. 689-698
Volume 33, Number 8, August 2019
- Gabriele Cruciani, Yvonne C. Martin, Andy Vinter, Richard Lewis, Federico Gago, Terry R. Stouch:
How computational chemistry develops: a tribute to Peter Goodford. 699-703 - Minh Khoa Nguyen, Léonard Jaillet, Stéphane Redon:
ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. 705-727 - Tomoyuki Miyao, Swarit Jasial, Jürgen Bajorath, Kimito Funatsu:
Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships. 729-743 - Saw Simeon, Nathjanan Jongkon, Warot Chotpatiwetchkul, Matthew Paul Gleeson:
Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies. 745-757 - Wen-Shan Liu, Wen-Yan Jin, Liang Zhou, Xing-Hua Lu, Wei-Ya Li, Ying Ma, Run-Ling Wang:
Structure based design of selective SHP2 inhibitors by De novo design, synthesis and biological evaluation. 759-774 - Kongkai Zhu, Jingwei Shao, Hongrui Tao, Xue Yan, Cheng Luo, Hua Zhang, Wenhu Duan:
Rational Design, synthesis and biological evaluation of novel triazole derivatives as potent and selective PRMT5 inhibitors with antitumor activity. 775-785
Volume 33, Number 9, September 2019
- Zoltán Orgován, György G. Ferenczy, György M. Keserü:
The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu5 receptor case study. 787-797 - Nizar A. Al-Shar'i, Qosay A. E. Al-Balas, Rand A. Al-Waqfi, Mohammad A. Hassan, Amer E. Alkhalifa, Nehad M. Ayoub:
Discovery of a nanomolar inhibitor of the human glyoxalase-I enzyme using structure-based poly-pharmacophore modelling and molecular docking. 799-815 - Jordane Preto, Francesco Gentile:
Assessing and improving the performance of consensus docking strategies using the DockBox package. 817-829 - Jonathan Cardoso-Silva, Lazaros G. Papageorgiou, Sophia Tsoka:
Network-based piecewise linear regression for QSAR modelling. 831-844 - Christian Bustamante, Rodrigo Ochoa, Claudia Asela, Carlos Muskus:
Repurposing of known drugs for leishmaniasis treatment using bioinformatic predictions, in vitro validations and pharmacokinetic simulations. 845-854 - Rino Ragno:
www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices - the Py-CoMFA web application as tool to build models from pre-aligned datasets. 855-864
Volume 33, Number 10, October 2019
- Ann E. Cleves, Stephen R. Johnson, Ajay N. Jain:
Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. 865-886 - Gabriele Macari, Daniele Toti, Fabio Polticelli:
Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. 887-903 - Dipankar Roy, Andriy Kovalenko:
Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent. 905-912 - Vijaya Kumar Hinge, Nikolay Blinov, Dipankar Roy, David S. Wishart, Andriy Kovalenko:
The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. 913-926 - Fanny S. Krebs, Jeremy Esque, Roland H. Stote:
A computational study of the molecular basis of antibiotic resistance in a DXR mutant. 927-940
Volume 33, Number 11, November 2019
- Daniel Reker, Richard A. Lewis:
Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine Learning. 941 - Edelmiro Moman, Maria A. Grishina, Vladimir Potemkin:
Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions. 943-953 - Galyna P. Volynets, Sergiy A. Starosyla, Mariia Yu. Rybak, Volodymyr G. Bdzhola, Oksana P. Kovalenko, Vasyl S. Vdovin, Sergiy M. Yarmoluk, Michail A. Tukalo:
Dual-targeted hit identification using pharmacophore screening. 955-964 - Vijaya Kumar Hinge, Dipankar Roy, Andriy Kovalenko:
Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors. 965-971 - Tejashree Redij, Jian Ma, Zhiyu Li, Xianxin Hua, Zhijun Li:
Discovery of a potential positive allosteric modulator of glucagon-like peptide 1 receptor through virtual screening and experimental study. 973-981 - Antonella Ciancetta, Priscila Rubio, David I. Lieberman, Kenneth A. Jacobson:
A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states. 983-996 - Stephen J. Barigye, José Manuel García de la Vega, Juan A. Castillo-Garit:
Undersampling: case studies of flaviviral inhibitory activities. 997-1008
Volume 33, Number 12, December 2019
- Michael K. Gilson:
This issue: Drug Design Data Resource Grand Challenge 4, first of two issues. 1009 - Lea El-Khoury, Diogo Santos-Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, David L. Mobley:
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. 1011-1020 - Junjie Zou, Chuan Tian, Carlos Simmerling:
Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. 1021-1029 - Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga:
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. 1031-1043 - Ashutosh Kumar, Kam Y. J. Zhang:
Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. 1045-1055 - Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov:
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. 1057-1069 - Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli:
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. 1071-1081 - Woong-Hee Shin, Daisuke Kihara:
Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0. 1083-1094 - Yuwei Yang, Jianing Lu, Chao Yang, Yingkai Zhang:
Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S. 1095-1105
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