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ORCIDJournal of Computer-Aided Molecular Design, Volume 37
Volume 37, Number 1, January 2023
- Christian Meyenburg
, Uschi Dolfus, Hans Briem, Matthias Rarey:
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. 1-16 - Kedan He, Djenerly G. Massena:
Examining unsupervised ensemble learning using spectroscopy data of organic compounds. 17-37 - Huaiqin Ma, Qingwen Shi, Xuhua Li, Junli Ren, Yuhan Wang, Zhijian Li, Lulu Ning:
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling. 39-51 - Jinhong Ren, Tasneem M. Vaid, Hyun Lee, Isabel Ojeda, Michael E. Johnson:
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations. 53-65
Volume 37, Number 2, February 2023
- Huafeng Xu:
The slow but steady rise of binding free energy calculations in drug discovery. 67-74 - Manuel A. Llanos, Lucas N. Alberca, María D. Ruiz, María L. Sbaraglini, Cristian Miranda, Agustina Pino-Martinez, Laura Fraccaroli, Carolina Carrillo, Catalina D. Alba Soto, Luciana Gavernet, Alan Talevi:
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity. 75-90 - Jiaqi Hu, Xianqiang Sun, Zhengzhong Kang, Jianxin Cheng:
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin. 91-105 - Kohei Umedera, Atsushi Yoshimori, Hengwei Chen, Hiroyuki Kouji, Hiroyuki Nakamura, Jürgen Bajorath:
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds. 107-115
Volume 37, Number 3, March 2023
- Talita Freitas de Freitas, Candida Deves Roth, Bruno Lopes Abbadi, Fernanda Souza Macchi Hopf, Marcia Alberton Perelló, Alexia de Matos Czeczot, Eduardo Vieira de Souza, Ana Flávia Borsoi, Pablo Machado, Cristiano Valim Bizarro, Luiz Augusto Basso, Luís Fernando S. M. Timmers:
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments. 117-128 - Anne Bonin, Floriane Montanari, Sebastian Niederführ, Andreas H. Göller:
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants. 129-145 - Jacob M. Remington, Kyle T. McKay, Noah B. Beckage, Jonathon B. Ferrell, Severin T. Schneebeli, Jianing Li:
GPCRLigNet: rapid screening for GPCR active ligands using machine learning. 147-156 - Fanglin Liang, Zhengzhong Kang, Xianqiang Sun, Jiao Chen, Xuemin Duan, Hu He, Jianxin Cheng:
Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study. 157-166
Volume 37, Number 4, April 2023
- Mackenzie Taylor, Junming Ho:
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn. 167-182 - Ekaterina A. Sosnina, Sergey Sosnin, Maxim V. Fedorov:
Improvement of multi-task learning by data enrichment: application for drug discovery. 183-200 - Nancy D. Pomarici, Franz Waibl, Patrick K. Quoika, Alexander Bujotzek, Guy Georges, Monica L. Fernández-Quintero, Klaus R. Liedl:
Structural mechanism of Fab domain dissociation as a measure of interface stability. 201-215 - Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. 217-225
Volume 37, Number 5, June 2023
- Haoxi Li, Nikhil M. Urs, Nicole Horenstein:
Computational insights into ligand-induced G protein and β-arrestin signaling of the dopamine D1 receptor. 227-244 - Marianna Stampolaki, Ioannis Stylianakis, Helen I. Zgurskaya, Antonios Kolocouris:
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations. 245-264 - João Carneiro, Rita P. Magalhães, Victor M. de la Oliva Roque, Manuel Simões, Diogo Pratas, Sergio F. Sousa:
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa. 265-278
Volume 37, Number 7, July 2023
- Julieta Reyna-Luna, Luis Soriano-Agueda, Christiaan Jardinez Vera, Marco Franco-Pérez:
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models. 279-299 - Yijing Zhang, Shiyao Chen, Taeyoung Choi, Yuzheng Qi, Qianhui Wang, Guanyi Li, Yaxue Zhao:
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1. 301-312 - Aida Shahraki, Jana Selent, Peter Kolb:
On the construction of LIECE models for the serotonin receptor 5-HT 2AR. 313-323 - Bo Liu, Juntao Ding, Yugang Liu, Jianzhang Wu, Xiaoping Wu, Qian Chen, Wulan Li:
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis. 325-338
Volume 37, Number 8, August 2023
- Rohith Anand Varikoti, Katherine J. Schultz, Chathuri J. Kombala, Agustin Kruel, Kristoffer R. Brandvold, Mowei Zhou, Neeraj Kumar:
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease. 339-355 - Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau:
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. 357-371 - Esben Jannik Bjerrum, Christian Margreitter, Thomas Blaschke, Simona Kolarova, Raquel Lopez-Rios de Castro:
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES. 373-394 - Michael Diedenhofen, Frank Eckert, Selman Terzi:
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge. 395-405
Volume 37, Number 9, September 2023
- Wemenes José Lima Silva, Renato Ferreira de Freitas:
Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors. 407-418 - A. S. Vinutha, Rajasekaran Ramalingam:
Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment. 419-434 - Gyoung Jin Park, Nam Sook Kang:
ADis-QSAR: a machine learning model based on biological activity differences of compounds. 435-451 - Jiwon Choi, Hyundo Lee, Soyoung Cho, Yorim Choi, Thuy X. Pham, Trang T. X. Huynh, Yun-Sook Lim, Soon B. Hwang:
Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing. 453-461
Volume 37, Number 10, October 2023
- Lu Zhang, Haiyan Liu:
Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function. 463-478 - Chonnikan Hanpaibool, Puey Ounjai, Sirilata Yotphan, Adrian J. Mulholland, James Spencer, Natharin Ngamwongsatit, Thanyada Rungrotmongkol:
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation. 479-489 - Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey:
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. 491-503 - Wemenes José Lima Silva, Renato Ferreira de Freitas:
Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors. 505
Volume 37, Number 11, November 2023
- Youjin Xiong, Yiqing Wang, Yisheng Wang, Chenmei Li, Yusong Peng, Junyu Wu, Lingyun Gu, Christopher J. Butch:
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation. 507-517 - Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller:
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design. 519-535 - Christian Jorgensen, Evan P. Troendle, Jakob P. Ulmschneider, Peter C. Searson, Martin B. Ulmschneider:
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium. 537-549 - Jaikee Kumar Singh, Jai Singh, Sandeep Kumar Srivastava:
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations. 551-563 - Luca Monari, Katia Galentino, Marco Cecchini:
ChemFlow_py: a flexible toolkit for docking and rescoring. 565-572
Volume 37, Number 12, December 2023
- Tanya Liyaqat, Tanvir Ahmad, Chandni Saxena:
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection. 573-584 - Anacleto Silva de Souza, Robson Francisco de Souza, Cristiane Rodrigues Guzzo:
Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). 585-606 - Ioannis Stylianakis, Nikolaos Zervos, Jenn-Huei Lii, Dimitrios A. Pantazis, Antonios Kolocouris:
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. 607-656 - Ioannis Stylianakis, Nikolaos Zervos, Jenn-Huei Lii, Dimitrios A. Pantazis, Antonios Kolocouris:
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. 657 - Nour Jamal Jaradat, Mámon M. Hatmal, Dana Alqudah, Mutasem Omar Taha:
Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study. 659-678 - Nour Jamal Jaradat, Mámon M. Hatmal, Dana Alqudah, Mutasem Omar Taha:
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study. 679 - Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea:
Exploring DrugCentral: from molecular structures to clinical effects. 681-694 - Qianqian Zhang, Jianting Han, Yongchang Zhu, Fansen Yu, Xiaopeng Hu, Henry H. Y. Tong, Huanxiang Liu:
Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. 695-706 - Roberto Paciotti, Alessandro Marrone, Cecilia Coletti, Nazzareno Re:
Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals. 707-719 - Martina Hrast Rambaher, Irena Zdovc, Nina Kocevar Glavac, Stanislav Gobec, Rok Frlan:
Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (-)-epicatechin. 721-733 - Gabriel Corrêa Veríssimo, Simone Queiroz Pantaleão, Philipe de Olveira Fernandes, Jadson Castro Gertrudes, Thales Kronenberger, Káthia Maria Honório, Vinicius Gonçalves Maltarollo:
MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling. 735-754 - Sohaib Habiballah, Janice Chambers, Edward Meek, Brad Reisfeld:
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases. 755-764 - Sadra Kashef Ol Gheta, Anne Bonin, Thomas Gerlach, Andreas H. Göller:
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state. 765-789 - Tiago O. Pereira, Maryam Abbasi, Rita I. Oliveira, Romina A. Guedes, Jorge A. R. Salvador, Joel P. Arrais:
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information. 791-806
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