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ORCIDJournal of Computer-Aided Molecular Design, Volume 35
Volume 35, Number 1, January 2021
- Martin Amezcua
, Lea El-Khoury, David L. Mobley:
SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. 1-35 - Piero Procacci, Guido Guarnieri:
SAMPL7 blind predictions using nonequilibrium alchemical approaches. 37-47 - Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys:
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. 49-61 - Yigitcan Eken, Nuno M. S. Almeida, Cong Wang, Angela K. Wilson:
SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics. 63-77 - Yuanjun Shi, Marie L. Laury, Zhi Wang, Jay W. Ponder:
AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. 79-93 - K. Kellett, David R. Slochower, Michael Schauperl, B. M. Duggan, Michael K. Gilson:
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. 95-104 - Zhaoxi Sun:
SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations. 105-115 - Zhe Huai, Huaiyu Yang, Xiao Li, Zhaoxi Sun:
SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations. 117-129
Volume 35, Number 2, February 2021
- Mehtap Isik, Ariën S. Rustenburg, Andrea Rizzi, Marilyn R. Gunner, David L. Mobley, John D. Chodera:
Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. 131-166 - Teresa Danielle Bergazin, Ido Y. Ben-Shalom, Nathan M. Lim, Sam C. Gill, Michael K. Gilson, David L. Mobley:
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. 167-177 - Akinori Sato, Tomoyuki Miyao, Swarit Jasial, Kimito Funatsu:
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations. 179-193 - Giuseppe Deganutti, Filippo Prischi, Christopher A. Reynolds:
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein. 195-207 - Dylan Serillon, Carles Bo, Xavier Barril:
Testing automatic methods to predict free binding energy of host-guest complexes in SAMPL7 challenge. 209-222 - Andrea Scarpino, László Petri, Damijan Knez, Tímea Imre, Péter Ábrányi-Balogh, György G. Ferenczy, Stanislav Gobec, György M. Keserü:
WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors. 223-244 - Alicia Rosell-Hidalgo, Luke Young, Anthony L. Moore, Taravat Ghafourian:
QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach. 245-260 - Dipankar Roy, Devjyoti Dutta, David S. Wishart, Andriy Kovalenko:
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet? 261-269
Volume 35, Number 3, March 2021
- Jordan N. Ehrman, Victoria T. Lim, Caitlin C. Bannan, Nam Thi, Daisy Y. Kyu, David L. Mobley:
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. 271-284 - Raquel Rodríguez-Pérez, Jürgen Bajorath:
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions. 285-295 - Noureddine Ben Khalaf, Susie Pham, Giuseppe Romeo, Sara Abdelghany, Sebastiano Intagliata, Peter Sedillo, Loredana Salerno, Jessica Gonzales, Dahmani M. Fathallah, Douglas J. Perkins, Ivy Hurwitz, Valeria Pittalà:
A computer-aided approach to identify novel Leishmania major protein disulfide isomerase inhibitors for treatment of leishmaniasis. 297-314 - Md. Mehedi Hasan, Md. Ashad Alam, Watshara Shoombuatong, Hiroyuki Kurata:
IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations. 315-323 - Wansiri Innok, Asadhawut Hiranrat, Netnapa Chana, Thanyada Rungrotmongkol, Panita Kongsune:
In silico and in vitro anti-AChE activity investigations of constituents from Mytragyna speciosa for Alzheimer's disease treatment. 325-336 - Neha Tripathi, Laurence Leherte, Daniel P. Vercauteren, Adèle D. Laurent:
Structure-based identification of inhibitors disrupting the CD2-CD58 interactions. 337-353 - Christopher M. Topham, Jeremy C. Smith:
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. 355-369 - Ki Hwan Kim:
Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. 371-396
Volume 35, Number 4, April 2021
- Andreas H. Göller:
Editorial special issue on "Quantum Mechanics in Industry". 397-398 - Anikó Udvarhelyi, Stephane Rodde, Rainer Wilcken:
ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules. 399-415 - Daniel S. Levine, Mark A. Watson, Leif D. Jacobson, Claire E. Dickerson, Haoyu S. Yu, Art D. Bochevarov:
Pattern-free generation and quantum mechanical scoring of ring-chain tautomers. 417-431 - Oleg Y. Borbulevych, Roger I. Martin, Lance M. Westerhoff:
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design. 433-451 - Nicolas Tielker, Lukas Eberlein, Gerhard Hessler, K. Friedemann Schmidt, Stefan Güssregen, Stefan M. Kast:
Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges? 453-472 - Rebecca Sure, Moad el Mahdali, Alex Plajer, Peter Deglmann:
Towards a converged strategy for including microsolvation in reaction mechanism calculations. 473-492 - Michael Edmund Beck, Jacopo Negroni, Svend Matthiesen, Michael Kohnen, Christoph Riplinger:
A binding mode hypothesis for prothioconazole binding to CYP51 derived from first principles quantum chemistry. 493-503 - Tobias A. Plöger, Stefan Koep, Hans-Christian Militzer, Andreas H. Göller:
Combined experimental and quantum mechanical elucidation of the synthetically accessible stereoisomers of Hydroxyestradienone (HED), the starting material for vilaprisan synthesis. 505-516 - Michael Schindler:
Investigations on the E/Z-isomerism of neonicotinoids. 517-529 - Markus R. Hermann, Alexander Pautsch, Marc A. Grundl, Alexander Weber, Christofer S. Tautermann:
Covalent inhibitor reactivity prediction by the electrophilicity index - in and out of scope. 531-539 - Mario Öeren, Peter J. Walton, Peter A. Hunt, David J. Ponting, Matthew D. Segall:
Predicting reactivity to drug metabolism: beyond P450s - modelling FMOs and UGTs. 541-555 - Tobias Morawietz, Nongnuch Artrith:
Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications. 557-586
Volume 35, Number 5, May 2021
- Atsushi Yoshimori, Huabin Hu, Jürgen Bajorath:
Adapting the DeepSARM approach for dual-target ligand design. 587-600 - Kensuke Misawa, Noriyuki Yamaotsu, Shuichi Hirono:
Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method. 601-611 - David T. Stanton, Jennifer R. Baker, Adam McCluskey, Stefan Paula:
Development and interpretation of a QSAR model for in vitro breast cancer (MCF-7) cytotoxicity of 2-phenylacrylonitriles. 613-628 - Kaori Sakaguchi, Yoshio Okiyama, Shigenori Tanaka:
In silico modeling of PAX8-PPARγ fusion protein in thyroid carcinoma: influence of structural perturbation by fusion on ligand-binding affinity. 629-642 - Zhe Huai, Huaiyu Yang, Zhaoxi Sun:
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations. 643-656 - Ammar Abdo, Maude Pupin:
LINGO-DL: a text-based approach for molecular similarity searching. 657-665 - Mahdi Ghorbani, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks:
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. 667-677 - Huizhen Ge, Longfei Mao, Jie Zhao, Yuwei Wang, Danfeng Shi, Xing Yang, Xiaorui Wang, Huanxiang Liu, Xiaojun Yao:
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays. 679-694
Volume 35, Number 6, June 2021
- Chiara Luise, Dina Robaa, Wolfgang Sippl:
Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study. 695-706 - Alberto Mills, Federico Gago:
Insight into the sequence-specific elements leading to increased DNA bending and ligase-mediated circularization propensity by antitumor trabectedin. 707-719 - Lorenzo Casbarra, Piero Procacci:
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges. 721-729 - Harutyun Sahakyan:
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring. 731-736 - Jean-Rémy Marchand, Bernard Pirard, Peter Ertl, Finton Sirockin:
CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities. 737-750 - Mariangela Agamennone, Loriano Storchi, Alessandro Marrone, Roberto Paciotti:
Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study. 751-770
Volume 35, Number 7, July 2021
- Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, Marilyn R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley:
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge. 771-802 - Antonio Viayna, Silvana Pinheiro, Carles Curutchet, F. Javier Luque, William J. Zamora:
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model. 803-811 - Judith Warnau, Karin Wichmann, Jens Reinisch:
COSMO-RS predictions of logP in the SAMPL7 blind challenge. 813-818 - Nazanin Donyapour, Alex Dickson:
Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method. 819-830 - Fabio Falcioni, Jas Kalayan, Richard H. Henchman:
Energy-entropy prediction of octanol-water logP of SAMPL7 N-acyl sulfonamide bioisosters. 831-840 - Basak Koca Findik, Zeynep Pinar Haslak, Evrim Arslan, Viktorya Aviyente:
SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules. 841-851 - Shujie Fan, Hristo Nedev, Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein:
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. 853-870
Volume 35, Number 8, August 2021
- Olivia Teixeira, Pedro Sousa Lacerda, Thamires Quadros Froes, Maria Cristina Nonato, Marcelo Santos Castilho:
Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy. 871-882 - Betsabeh Tanoori, Mansoor Zolghadri Jahromi, Eghbal G. Mansoori:
Binding affinity prediction for binary drug-target interactions using semi-supervised transfer learning. 883-900 - Eelke B. Lenselink, Pieter F. W. Stouten:
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge. 901-909 - Hafiz Saqib Ali, Arghya Chakravorty, Jas Kalayan, Sam P. de Visser, Richard H. Henchman:
Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge. 911-921 - Kenneth Lopez, Silvana Pinheiro, William J. Zamora:
Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge. 923-931 - Nicolas Tielker, Stefan Güssregen, Stefan M. Kast:
SAMPL7 physical property prediction from EC-RISM theory. 933-941
Volume 35, Number 9, September 2021
- Ignacio Lizana, Elena A. Uribe, Eduardo J. Delgado:
A theoretical approach for the acylation/deacylation mechanisms of avibactam in the reversible inhibition of KPC-2. 943-952 - Robert M. Raddi, Vincent A. Voelz:
Stacking Gaussian processes to improve pKa predictions in the SAMPL7 challenge. 953-961 - Yuhang Wang, Sruthi Murlidaran, David A. Pearlman:
Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands. 963-971 - Mazen Y. Hamed, Reema Siam, Roza Zaid:
The role of zinc finger linkers in zinc finger protein binding to DNA. 973-986 - François Van Liefferinge, Eva-Maria Krammer, Jehan Waeytens, Martine Prévost:
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study. 987-1007
Volume 35, Number 10, October 2021
- Spencer J. Sabatino, Andrew S. Paluch:
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol. 1009-1024 - Iva Lukac, Paul G. Wyatt, Ian H. Gilbert, Fabio Zuccotto:
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method. 1025-1036 - Aijaz Ahmad Malik, Warot Chotpatiwetchkul, Chuleeporn Phanus-umporn, Chanin Nantasenamat, Phasit Charoenkwan, Watshara Shoombuatong:
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors. 1037-1053 - Piero Procacci, Marina Macchiagodena:
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. 1055-1065 - Jorge Enrique Hernández González, Emir Salas-Sarduy, Lilian Hernández Alvarez, Diego Enry Barreto Gomes, Pedro Geraldo Pascutti, Chris Oostenbrink, Vitor B. P. Leite:
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. 1067-1079
Volume 35, Number 11, November 2021
- R. Bruno Hernández-Alvarado, Abraham Madariaga-Mazón, Fernando Cosme-Vela, Andrés F. Marmolejo-Valencia, Adel Nefzi, Karina Martínez-Mayorga:
Encoding mu-opioid receptor biased agonism with interaction fingerprints. 1081-1093 - Omar N. A. Demerdash:
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction. 1095-1123 - Samar Mahmoud, Benedict W. J. Irwin, Dmitriy Chekmarev, Shyam Vyas, Jeff Kattas, Thomas M. Whitehead, Tamsin Mansley, Jack Bikker, Gareth John Conduit, Matthew D. Segall:
Imputation of sensory properties using deep learning. 1125-1140 - Matthew N. Bahr, Aakankschit Nandkeolyar, John K. Kenna, Neysa Nevins, Luigi Da Vià, Mehtap Isik, John D. Chodera, David L. Mobley:
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. 1141-1155
Volume 35, Number 12, December 2021
- Javed Iqbal, Martin Vogt, Jürgen Bajorath:
Prediction of activity cliffs on the basis of images using convolutional neural networks. 1157-1164 - Mesfer Al Shahrani, Mohammad Abohassan, Mohammad Y. Alshahrani, Abdulrahim R. Hakami, Prasanna Rajagopalan:
High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma. 1165-1176 - Vasyl V. Kovalishyn, Volodymyr Zyabrev, Maryna V. Kachaeva, Kostiantyn Ziabrev, Kathy Keith, Emma Harden, Caroll Hartline, Scott H. James, Volodymyr Brovarets:
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing. 1177-1187 - Richard A. Lewis:
Best practices for repurposing studies. 1189-1193 - Emilie Pihan, Martin Kotev, Obdulia Rabal, Claudia Beato, Constantino Diaz Gonzalez:
Fine tuning for success in structure-based virtual screening. 1195-1206
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