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ORCIDJournal of Computer-Aided Molecular Design, Volume 34
Volume 34, Number 1, January 2020
- Filip Miljkovic
, Jürgen Bajorath:
Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome. 1-10 - Xiaoqian Xu, Li Zhang, Ying Cai, Dongxin Liu, Zhengwen Shang, Qiuhong Ren, Qiong Li, Weidong Zhao, Yuhua Chen:
Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening. 11-25 - Chonnikan Hanpaibool, Matina Leelawiwat, Kaito Takahashi, Thanyada Rungrotmongkol:
Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. 27-37 - Radhika Vangala, Sree Kanth Sivan, Saikiran Reddy Peddi, Vijjulatha Manga:
Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120. 39-54 - Maxim Gureev, Daria Novikova, Tatyana Grigoreva, Svetlana Vorona, Alexander Garabadzhiu, Vyacheslav Tribulovich:
Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein-protein interaction. 55-70 - Andreas Mecklenfeld, Gabriele Raabe:
Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies. 71-82 - Lakshmi Maganti, Dhananjay Bhattacharyya:
Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches. 83-95
Volume 34, Number 2, February 2020
- Michael K. Gilson, Rommie E. Amaro:
Drug Design Data Resource, Grand Challenge 4, second of two issues. 97 - Conor D. Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia B. McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson:
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. 99-119 - Oleg V. Stroganov, Fedor N. Novikov, Michael G. Medvedev, Artem O. Dmitrienko, Igor S. Gerasimov, Igor V. Svitanko, Ghermes G. Chilov:
The role of human in the loop: lessons from D3R challenge 4. 121-130 - Duc Duy Nguyen, Kaifu Gao, Menglun Wang, Guo-Wei Wei:
MathDL: mathematical deep learning for D3R Grand Challenge 4. 131-147 - Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. 149-162 - Sukanya Sasmal, Lea El-Khoury, David L. Mobley:
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. 163-177 - Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos A. Coutsias, Ken A. Dill, Dima Kozakov:
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. 179-189 - Maria Kadukova, Vladimir Chupin, Sergei Grudinin:
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4. 191-200 - Bo Wang, Ho-Leung Ng:
Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4. 201-217
Volume 34, Number 3, March 2020
- George Nicola, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Druggable exosites of the human kino-pocketome. 219-230 - Gustav Olanders, Hiba Alogheli, Peter Brandt, Anders Karlén:
Conformational analysis of macrocycles: comparing general and specialized methods. 231-252 - Alberto Mills, Federico Gago:
Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. 253-265 - Jesús Sánchez-Márquez, Victor García, David Zorrilla, Manuel Fernández:
Software to obtain spatially localized functions from different radial functions. 267-280 - G. I. Makarov, T. M. Makarova:
A noncanonical binding site of linezolid revealed via molecular dynamics simulations. 281-291 - Martiniano Bello, Concepción Guadarrama-García, Rolando Alberto Rodriguez-Fonseca:
Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2. 293-303 - Gonzalo Cerruela García, José Pérez-Parras Toledano, Aida de Haro-García, Nicolás García-Pedrajas:
Influence of feature rankers in the construction of molecular activity prediction models. 305-325
Volume 34, Number 4, April 2020
- Maximiliano Riquelme, Esteban Vöhringer-Martinez:
SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges. 327-334 - Mehtap Isik, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley:
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. 335-370 - Piero Procacci, Guido Guarnieri:
SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. 371-384 - Christoph Loschen, Jens Reinisch, Andreas Klamt:
COSMO-RS based predictions for the SAMPL6 logP challenge. 385-392 - Shuzhe Wang, Sereina Riniker:
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. 393-403 - Mehtap Isik, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera:
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. 405-420 - Ye Ding, You Xu, Cheng Qian, Jinfeng Chen, Jian Zhu, Houhou Huang, Yi Shi, Jing Huang:
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields. 421-435 - Alexei M. Nikitin:
Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances. 437-441 - William J. Zamora, Silvana Pinheiro, Kilian German, Clara Pérez-Ràfols, Carles Curutchet, F. Javier Luque:
Prediction of the n-octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations. 443-451 - Nicolas Tielker, Daniel Tomazic, Lukas Eberlein, Stefan Güssregen, Stefan M. Kast:
The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory. 453-461 - Evrim Arslan, Basak Koca Findik, Viktorya Aviyente:
A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach. 463-470
Volume 34, Number 5, May 2020
- Andreas Krämer, Phillip S. Hudson, Michael R. Jones, Bernard R. Brooks:
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. 471-483 - Michael R. Jones, Bernard R. Brooks:
Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. 485-493 - Prajay Patel, David M. Kuntz, Michael R. Jones, Bernard R. Brooks, Angela K. Wilson:
SAMPL6 logP challenge: machine learning and quantum mechanical approaches. 495-510 - Davy Guan, Raymond Lui, Slade Matthews:
LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge molecules. 511-522 - Raymond Lui, Davy Guan, Slade Matthews:
A comparison of molecular representations for lipophilicity quantitative structure-property relationships with results from the SAMPL6 logP Prediction Challenge. 523-534 - Samarjeet Prasad, Bernard R. Brooks:
A deep learning approach for the blind logP prediction in SAMPL6 challenge. 535-542 - Shujie Fan, Bogdan I. Iorga, Oliver Beckstein:
Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. 543-560 - Marilyn R. Gunner, Taichi Murakami, Ariën S. Rustenburg, Mehtap Isik, John D. Chodera:
Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states. 561-573 - Jonathan A. Ouimet, Andrew S. Paluch:
Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models. 575-588 - Zhaoxi Sun, Qiao-Le He, Xiao Li, Zhengdan Zhu:
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations. 589-600 - Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera:
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. 601-633
Volume 34, Number 6, June 2020
- Piero Procacci:
A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge. 635-639 - Vikram Khanna, Jacob I. Monroe, Michael F. Doherty, Baron Peters:
Performing solvation free energy calculations in LAMMPS using the decoupling approach. 641-646 - Takeshi Ashida, Takeshi Kikuchi:
A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems. 647-658 - Edgar López-López, Obdulia Rabal, Julen Oyarzabal, José L. Medina-Franco:
Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach. 659-669 - Ravi Kumar Rajan, Muthiah Ramanathan:
Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assay. 671-682 - Petr Kovár, Jakub Skoda, Miroslav Pospísil, Klára Melánová, Jan Svoboda, Ludvík Benes, Petr Kutálek, Vítezslav Zima, Filip Bures:
How N-(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives are arranged in the interlayer space of zirconium sulfophenylphosphonate: a problem solved by experimental and calculation methods. 683-695 - Kamil J. Kuder, Ilona Michalik, Katarzyna Kiec-Kononowicz, Peter Kolb:
A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands. 697-707
Volume 34, Number 7, July 2020
- Nathan Brown, Peter Ertl, Richard A. Lewis, Torsten Luksch, Daniel Reker, Nadine Schneider:
Artificial intelligence in chemistry and drug design. 709-715 - Matthew C. Robinson, Robert C. Glen, Alpha A. Lee:
Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction. 717-730 - Henry E. Webel, Talia B. Kimber, Silke Radetzki, Martin Neuenschwander, Marc Nazaré, Andrea Volkamer:
Revealing cytotoxic substructures in molecules using deep learning. 731-746 - Darren V. S. Green, Stephen D. Pickett, Christopher N. Luscombe, Stefan Senger, David Marcus, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson:
BRADSHAW: a system for automated molecular design. 747-765 - Darren V. S. Green, Stephen D. Pickett, Christopher N. Luscombe, Stefan Senger, David Marcus, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson:
Correction to: BRADSHAW: a system for automated molecular design. 767 - Zhonghua Xia, Pavel Karpov, Grzegorz M. Popowicz, Igor V. Tetko:
Focused Library Generator: case of Mdmx inhibitors. 769-782 - Gian Marco Ghiandoni, Michael J. Bodkin, Beining Chen, Dimitar Hristozov, James E. A. Wallace, James Webster, Valerie J. Gillet:
Enhancing reaction-based de novo design using a multi-label reaction class recommender. 783-803 - Arkadii I. Lin, Bernd Beck, Dragos Horvath, Gilles Marcou, Alexandre Varnek:
Diversifying chemical libraries with generative topographic mapping. 805-815
Volume 34, Number 8, August 2020
- Anjali Soni, Ruchika Bhat, Bhyravabhotla Jayaram:
Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method. 817-830 - Anita Rácz, György M. Keserü:
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling. 831-839 - Muhammad Arif, Saeed Ahmad, Farman Ali, Ge Fang, Min Li, Dong-Jun Yu:
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree. 841-856 - Yudibeth Sixto-López, Martiniano Bello, José Correa-Basurto:
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. 857-878 - Huiqun Wang, Bethany A. Reinecke, Yan Zhang:
Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators. 879-895 - Roberto Paciotti, Mariangela Agamennone, Cecilia Coletti, Loriano Storchi:
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach. 897-914 - Bani Kumar Pathak, Debajyoti Das, Sayan Bhakta, Partha Chakrabarti, Jayati Sengupta:
Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form. 915-927
Volume 34, Number 9, September 2020
- Dagmar Stumpfe, Huabin Hu, Jürgen Bajorath:
Advances in exploring activity cliffs. 929-942 - Huabin Hu, Jürgen Bajorath:
Simplified activity cliff network representations with high interpretability and immediate access to SAR information. 943-952 - Matthew P. Baumgartner, David A. Evans:
Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis. 953-963 - Metin Yazar, Pemra Ozbek:
Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy. 965-974 - Izudin Redzepovic, Boris Furtula:
Predictive potential of eigenvalue-based topological molecular descriptors. 975-982 - Manish Kumar Tripathi, Piyoosh Sharma, Avanish Tripathi, Prabhash Nath Tripathi, Pavan Srivastava, Ankit Seth, Sushant Kumar Shrivastava:
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer's disease. 983-1002 - Shalini Thiruchittampalam, Samantha Weerasinghe:
Plausible compounds drawn from plants as curative agents for neurodegeneration: An in-silico approach. 1003-1011
Volume 34, Number 10, October 2020
- Raquel Rodríguez-Pérez, Jürgen Bajorath:
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions. 1013-1026 - Gregory L. Szwabowski, Paige N. Castleman, Chandler K. Sears, Lee H. Wink, Judith A. Cole, Daniel L. Baker, Abby L. Parrill:
Benchmarking GPCR homology model template selection in combination with de novo loop generation. 1027-1044 - Almudena Perona, M. Piedad Ros, Alberto Mills, Antonio Morreale, Federico Gago:
Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1. 1045-1062 - Isaias Lans, Karen Palacio-Rodríguez, Claudio N. Cavasotto, Pilar Cossio:
Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. 1063-1077 - José L. Borioni, Valeria Cavallaro, Adriana B. Pierini, Ana Paula Murray, Alicia B. Peñéñory, Marcelo Puiatti, Manuela E. García:
An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme. 1079-1090 - Natalie M. Colodette, Lucas S. Franco, Rodolfo C. Maia, Harold H. Fokoue, Carlos Mauricio R. Sant'Anna, Eliezer J. Barreiro:
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models. 1091-1103 - Phasit Charoenkwan, Chanin Nantasenamat, Md. Mehedi Hasan, Watshara Shoombuatong:
Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation. 1105-1116
Volume 34, Number 11, November 2020
- Robert D. Clark, Denise N. Morris, Gary Chinigo, Michael S. Lawless, Jacques Prudhomme, Karine G. Le Roch, Maria José Lafuente, Santiago Ferrer, Francisco Javier Gamo, Robert Gadwood, Walter S. Woltosz:
Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones. 1117-1132 - Mei Qian Yau, Abigail L. Emtage, Jason S. E. Loo:
Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset. 1133-1145 - Ammar Abdo, Eissa Ghaleb, Naser K. A. Alajmi, Maude Pupin:
Monomer structure fingerprints: an extension of the monomer composition version for peptide databases. 1147-1156 - Denis B. Tikhonov, Lianyun Lin, Daniel S. C. Yang, Zhiguang Yuchi, Boris S. Zhorov:
Phenylalkylamines in calcium channels: computational analysis of experimental structures. 1157-1169 - Marianna Bufano, Marion Laudette, Jean-Paul Blondeau, Frank Lezoualc'h, Marianna Nalli, Romano Silvestri, Andrea Brancale, Antonio Coluccia:
Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics. 1171-1179 - Silvia Atanasio, Giuseppe Deganutti, Christopher A. Reynolds:
Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics. 1181-1193 - Kai Liu, Hironori Kokubo:
Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations. 1195-1205
Volume 34, Number 12, December 2020
- Dimitar G. Yonchev, Jürgen Bajorath:
DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology. 1207-1218 - Brian Olson, Anthony Cruz-Balberdy, Lieyang Chen, Mossa Ghattas, Yeonji Ji, Kunhui Huang, Steven Ayoub, Tyler Luchko, Daniel J. McKay, Tom Kurtzman:
An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. 1219-1228 - Mst. Shamima Khatun, Md. Mehedi Hasan, Watshara Shoombuatong, Hiroyuki Kurata:
ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations. 1229-1236 - Sara Sarfaraz, Iqra Muneer, Haiyan Liu:
Combining fragment docking with graph theory to improve ligand docking for homology model structures. 1237-1259 - Hossein Aghazadeh, Mokhtar Ganjali Koli, Reza Ranjbar, Kamran Pooshang Bagheri:
Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study. 1261-1273 - Julián A. Bélgamo, Lucas N. Alberca, Jorge L. Pórfido, Franco N. Caram Romero, Santiago Rodriguez, Alan Talevi, Betina Córsico, Gisela R. Franchini:
Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets. 1275-1288 - Jianzhong Chen, Wei Wang, Haibo Sun, Laixue Pang, Baohua Yin:
Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics. 1289-1305
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