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Journal 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 Oliveira 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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