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SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-03-17 Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey
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Molecular dynamics simulations as a guide for modulating small molecule aggregation J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-03-12 Azam Nesabi, Jas Kalayan, Sara Al-Rawashdeh, Mohammad A. Ghattas, Richard A. Bryce
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Molecule auto-correction to facilitate molecular design J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-02-16 Alan Kerstjens, Hans De Winter
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Rethinking the applicability domain analysis in QSAR models J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-02-14 Jose R. Mora, Edgar A. Marquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Perez-Castillo, Guillermin Agüero-Chapin, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J. Barigye
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Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-02-07 Md Fulbabu Sk, Sunanda Samanta, Sayan Poddar, Parimal Kar
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A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-01-31 Florian Führer, Andrea Gruber, Holger Diedam, Andreas H. Göller, Stephan Menz, Sebastian Schneckener
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Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2024-01-24 Maria Lazou, Jonathan R. Hutton, Arijit Chakravarty, Diane Joseph-McCarthy
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Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-12-16 Aleksei Kabedev, Christel A. S. Bergström, Per Larsson
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QM assisted ML for 19F NMR chemical shift prediction J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-12-12 Patrick Penner, Anna Vulpetti
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Open-ComBind: harnessing unlabeled data for improved binding pose prediction J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-12-08 Andrew T. McNutt, David Ryan Koes
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Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-11-21 Adan Gallardo, Bercem Dutagaci
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Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-25 Sadra Kashef Ol Gheta, Anne Bonin, Thomas Gerlach, Andreas H. Göller
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Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-17 Tiago O. Pereira, Maryam Abbasi, Rita I. Oliveira, Romina A. Guedes, Jorge A. R. Salvador, Joel P. Arrais
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MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-07 Gabriel Corrêa Veríssimo, Simone Queiroz Pantaleão, Philipe de Olveira Fernandes, Jadson Castro Gertrudes, Thales Kronenberger, Kathia Maria Honorio, Vinícius Gonçalves Maltarollo
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Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (–)-epicatechin J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-05 Martina Hrast Rambaher, Irena Zdovc, Nina Kočevar Glavač, Stanislav Gobec, Rok Frlan
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The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-05 Sohaib Habiballah, Janice Chambers, Edward Meek, Brad Reisfeld
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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) J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-04 Anacleto Silva de Souza, Robson Francisco de Souza, Cristiane Rodrigues Guzzo
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TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-09-30 Tanya Liyaqat, Tanvir Ahmad, Chandni Saxena
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Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors. J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-10-01 Wemenes José Lima Silva,Renato Ferreira de Freitas
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Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-09-25 R. Paciotti, A. Marrone, C. Coletti, N. Re
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Exploring DrugCentral: from molecular structures to clinical effects J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-09-14 Liliana Halip, Sorin Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
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Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-29 Qianqian Zhang, Jianting Han, Yongchang Zhu, Fansen Yu, Xiaopeng Hu, Henry H. Y. Tong, Huanxiang Liu
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ChemFlow_py: a flexible toolkit for docking and rescoring J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-24 Luca Monari, Katia Galentino, Marco Cecchini
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Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-19 Ioannis Stylianakis, Nikolaos Zervos, Jenn-Huei Lii, Dimitrios A. Pantazis, Antonios Kolocouris
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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 J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-19 Nour Jamal Jaradat, Mamon Hatmal, Dana Alqudah, Mutasem Omar Taha
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A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-12 Christian Jorgensen, Evan P. Troendle, Jakob P. Ulmschneider, Peter C. Searson, Martin B. Ulmschneider
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Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-08 Youjin Xiong, Yiqing Wang, Yisheng Wang, Chenmei Li, Peng Yusong, Junyu Wu, Yiqing Wang, Lingyun Gu, Christopher J. Butch
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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 J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-05 Jaikee Kumar Singh, Jai Singh, Sandeep Kumar Srivastava
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Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-08-03 Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller
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PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-07-29 Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey
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Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-07-27 Lu Zhang, Haiyan Liu
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Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-07-24 Chonnikan Hanpaibool, Puey Ounjai, Sirilata Yotphan, Adrian J. Mulholland, James Spencer, Natharin Ngamwongsatit, Thanyada Rungrotmongkol
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Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-07-15 Jiwon Choi, Hyundo Lee, Soyoung Cho, Yorim Choi, Thuy X. Pham, Trang T. X. Huynh, Yun-Sook Lim, Soon B. Hwang
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ADis-QSAR: a machine learning model based on biological activity differences of compounds J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-29 Gyoung Jin Park, Nam Sook Kang
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Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-27 A. S. Vinutha, R. Rajasekaran
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COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-27 Michael Diedenhofen, Frank Eckert, Selman Terzi
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Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-28 Wemenes José Lima Silva, Renato Freitas de Freitas
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Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-17 Esben Jannik Bjerrum, Christian Margreitter, Thomas Blaschke, Simona Kolarova, Raquel López-Ríos de Castro
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Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-14 Rohith Anand Varikoti, Katherine J. Schultz, Chathuri J. Kombala, Agustin Kruel, Kristoffer R. Brandvold, Mowei Zhou, Neeraj Kumar
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On the construction of LIECE models for the serotonin receptor 5-HT $$_{\text {2A}}$$ R J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-14 Aida Shahraki, Jana Selent, Peter Kolb
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OFraMP: a fragment-based tool to facilitate the parametrization of large molecules J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-13 Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen M. 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
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Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1 J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-07 Yijing Zhang, Shiyao Chen, Taeyoung Choi, Yuzheng Qi, Qianhui Wang, Guanyi Li, Yaxue Zhao
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Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-06-03 Bo Liu, Juntao Ding, Yugang Liu, Jianzhang Wu, Xiaoping Wu, Qian Chen, Wulan Li
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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 J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-05-28 Julieta Reyna-Luna, Luis Soriano-Agueda, Christiaan Jardinez Vera, Marco Franco-Pérez
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Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-05-02 Marianna Stampolaki, Ioannis Stylianakis, Helen I. Zgurskaya, Antonios Kolocouris
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TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-04-22 João Carneiro, Rita P. Magalhães, Victor M. de la Oliva Roque, Manuel Simões, Diogo Pratas, Sérgio F. Sousa
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Computational insights into ligand–induced G protein and β-arrestin signaling of the dopamine D1 receptor J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-04-15 Haoxi Li, Nikhil M. Urs, Nicole Horenstein
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Improvement of multi-task learning by data enrichment: application for drug discovery J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-03-21 Ekaterina A. Sosnina, Sergey Sosnin, Maxim V. Fedorov
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Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-03-21 Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
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MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-03-17 Mackenzie Taylor, Junming Ho
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Structural mechanism of Fab domain dissociation as a measure of interface stability J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-03-15 Nancy D. Pomarici, Franz Waibl, Patrick K. Quoika, Alexander Bujotzek, Guy Georges, Monica L. Fernández-Quintero, Klaus R. Liedl
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Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-02-28 Fanglin Liang, Zhengzhong Kang, Xianqiang Sun, Jiao Chen, Xuemin Duan, Hu He, Jianxin Cheng
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GPCRLigNet: rapid screening for GPCR active ligands using machine learning J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-02-25 Jacob M Remington, Kyle T McKay, Noah B Beckage, Jonathon B Ferrell, Severin T. Schneebeli, Jianing Li
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pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2023-02-17 Anne Bonin, Floriane Montanari, Sebastian Niederführ, Andreas H. Göller
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Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-12-22 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, Luis Fernando Saraiva Macedo Timmers
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A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-12-10 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
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The slow but steady rise of binding free energy calculations in drug discovery J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-12-05 Huafeng Xu
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DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-12-03 Kohei Umedera, Atsushi Yoshimori, Hengwei Chen, Hiroyuki Kouji, Hiroyuki Nakamura, Jürgen Bajorath
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Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-12-02 Jiaqi Hu, Xianqiang Sun, Zhengzhong Kang, Jianxin Cheng
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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 J. Comput. Aid. Mol. Des. (IF 3.5) Pub Date : 2022-11-25 Jinhong Ren, Tasneem M. Vaid, Hyun Lee, Isabel Ojeda, Michael E. Johnson