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(2024, February) Journal of Chemical Information and Modeling Vol. 64 (3) American Chemical Society (ACS)

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Reference TypeJournal (issue)
JournalJournal of Chemical Information and ModelingISSN1549-9596
Year2024 (February)Volume64
Issue<   3   >
PublisherAmerican Chemical Society (ACS)
Mindat Ref. ID17156746Long-form Identifiermindat:1:5:17156746:7
GUID0
Full Reference(2024, February) Journal of Chemical Information and Modeling Vol. 64 (3) American Chemical Society (ACS)
Plain Text(2024, February) Journal of Chemical Information and Modeling Vol. 64 (3) American Chemical Society (ACS)
In(2024) Journal of Chemical Information and Modeling Vol. 64. American Chemical Society (ACS)

Contains

(2024) Issue Editorial Masthead. Journal of Chemical Information and Modeling, 64 (3) doi:10.1021/civ064i003_1768946
(2024) Issue Publication Information. Journal of Chemical Information and Modeling, 64 (3) doi:10.1021/civ064i003_1768945
Zhang, Jinlu, Fang, Yin, Shao, Xin, Chen, Huajun, Zhang, Ningyu, Fan, Xiaohui (2024) The Future of Molecular Studies through the Lens of Large Language Models. Journal of Chemical Information and Modeling, 64 (3) 563-566 doi:10.1021/acs.jcim.3c01977
Jansen, Anton, Aho, Noora, Groenhof, Gerrit, Buslaev, Pavel, Hess, Berk (2024) phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64 (3) 567-574 doi:10.1021/acs.jcim.3c01313
Shen, Tao, Guo, Jiale, Han, Zunsheng, Zhang, Gao, Liu, Qingxin, Si, Xinxin, Wang, Dongmei, Wu, Song, Xia, Jie (2024) AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. Journal of Chemical Information and Modeling, 64 (3) 575-583 doi:10.1021/acs.jcim.3c01562
Torrens-Fontanals, Mariona, Tourlas, Panagiotis, Doerr, Stefan, De Fabritiis, Gianni (2024) PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data. Journal of Chemical Information and Modeling, 64 (3) 584-589 doi:10.1021/acs.jcim.3c01776
Horne, Robert I., Wilson-Godber, Jared, González Díaz, Alicia, Brotzakis, Z. Faidon, Seal, Srijit, Gregory, Rebecca C., Possenti, Andrea, Chia, Sean, Vendruscolo, Michele (2024) Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. Journal of Chemical Information and Modeling, 64 (3) 590-596 doi:10.1021/acs.jcim.3c01777
Nicolle, Andre, Deng, Sili, Ihme, Matthias, Kuzhagaliyeva, Nursulu, Ibrahim, Emad Al, Farooq, Aamir (2024) Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. Journal of Chemical Information and Modeling, 64 (3) 597-620 doi:10.1021/acs.jcim.3c01633
Gartan, Parveen, Khorsand, Fahimeh, Mizar, Pushpak, Vahokovski, Juha Ilmari, Cervantes, Luis F., Haug, Bengt Erik, Brenk, Ruth, Brooks, Charles L., Reuter, Nathalie (2024) Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of Chemical Information and Modeling, 64 (3) 621-626 doi:10.1021/acs.jcim.3c01949
Huang, Hongshuo, Magar, Rishikesh, Barati Farimani, Amir (2024) Pretraining Strategies for Structure Agnostic Material Property Prediction. Journal of Chemical Information and Modeling, 64 (3) 627-637 doi:10.1021/acs.jcim.3c00919
Tiwari, Surya Prakash, Shi, Wei, Budhathoki, Samir, Baker, James, Sekizkardes, Ali K., Zhu, Lingxiang, Kusuma, Victor A., Hopkinson, David P., Steckel, Janice A. (2024) Creation of Polymer Datasets with Targeted Backbones for Screening of High-Performance Membranes for Gas Separation. Journal of Chemical Information and Modeling, 64 (3) 638-652 doi:10.1021/acs.jcim.3c01232
Kyro, Gregory W., Morgunov, Anton, Brent, Rafael I., Batista, Victor S. (2024) ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. Journal of Chemical Information and Modeling, 64 (3) 653-665 doi:10.1021/acs.jcim.3c01456
Zhang, Hao, Huang, Jinchao, Xie, Junjie, Huang, Weifeng, Yang, Yuedong, Xu, Mingyuan, Lei, Jinping, Chen, Hongming (2024) GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of Chemical Information and Modeling, 64 (3) 666-676 doi:10.1021/acs.jcim.3c01700
Kim, Hyeonsu, Lee, Kyunghoon, Kim, Jun Hyeong, Kim, Woo Youn (2024) Deep Learning-Based Chemical Similarity for Accelerated Organic Light-Emitting Diode Materials Discovery. Journal of Chemical Information and Modeling, 64 (3) 677-689 doi:10.1021/acs.jcim.3c01747
Geer, Lewis Y., Stein, Stephen E., Mallard, William Gary, Slotta, Douglas J. (2024) AIRI: Predicting Retention Indices and Their Uncertainties Using Artificial Intelligence. Journal of Chemical Information and Modeling, 64 (3) 690-696 doi:10.1021/acs.jcim.3c01758
Tossou, Prudencio, Wognum, Cas, Craig, Michael, Mary, Hadrien, Noutahi, Emmanuel (2024) Real-World Molecular Out-Of-Distribution: Specification and Investigation. Journal of Chemical Information and Modeling, 64 (3) 697-711 doi:10.1021/acs.jcim.3c01774
Sanchez, Alec J., Maier, Sarah, Raghavachari, Krishnan (2024) Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning. Journal of Chemical Information and Modeling, 64 (3) 712-723 doi:10.1021/acs.jcim.3c01923
Ma, Minfei, Zhang, Xinben, Zhou, Liping, Han, Zijian, Shi, Yulong, Li, Jintian, Wu, Leyun, Xu, Zhijian, Zhu, Weiliang (2024) D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. Journal of Chemical Information and Modeling, 64 (3) 724-736 doi:10.1021/acs.jcim.3c01657
Bo, Weichen, Duan, Yangqin, Zou, Yurong, Ma, Ziyan, Yang, Tao, Wang, Peng, Guo, Tao, Fu, Zhiyuan, Wang, Jianmin, Fan, Linchuan, liu, Jie, Wang, Taijin, Chen, Lijuan (2024) Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors. Journal of Chemical Information and Modeling, 64 (3) 737-748 doi:10.1021/acs.jcim.3c01818
Das, Susanta, Merz, Kenneth M. (2024) Molecular Gas-Phase Conformational Ensembles. Journal of Chemical Information and Modeling, 64 (3) 749-760 doi:10.1021/acs.jcim.3c01309
Wang, Qing, Fu, Xuegang, Yan, Yuting, Liu, Tao, Xie, Yuting, Song, Xiaoqing, Zhou, Yu, Xu, Min, Wang, Ping, Fu, Peng, Huang, Jianhui, Huang, Niu (2024) Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. Journal of Chemical Information and Modeling, 64 (3) 761-774 doi:10.1021/acs.jcim.3c01282
Kirkland, Justin K., Kumawat, Jugal, Shaban Tameh, Maliheh, Tolman, Tyson, Lambert, Allison C., Lief, Graham R., Yang, Qing, Ess, Daniel H. (2024) Machine Learning Models for Predicting Zirconocene Properties and Barriers. Journal of Chemical Information and Modeling, 64 (3) 775-784 doi:10.1021/acs.jcim.3c01575
Tong, Mingqiong, Liu, Peng, Li, Chaoqun, Zhang, Zhongyu, Sun, Wan, Dong, Pingxuan, Fan, Na, Wang, Xiaoyue, Liu, Jing, Lv, Chao, Cao, Zanxia, Wang, Yan (2024) Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. Journal of Chemical Information and Modeling, 64 (3) 785-798 doi:10.1021/acs.jcim.3c01584
Deb, Jyotirmoy, Saikia, Lakshi, Dihingia, Kripa Dristi, Sastry, G. Narahari (2024) ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT. Journal of Chemical Information and Modeling, 64 (3) 799-811 doi:10.1021/acs.jcim.3c01702
Landry, Luke, Li, Pengfei (2024) Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of Chemical Information and Modeling, 64 (3) 812-824 doi:10.1021/acs.jcim.3c01815
Hölzer, Christian, Gordiy, Igor, Grimme, Stefan, Bursch, Markus (2024) Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set. Journal of Chemical Information and Modeling, 64 (3) 825-836 doi:10.1021/acs.jcim.3c01832
Kharche, Shalmali, Yadav, Manjul, Hande, Vrushali, Prakash, Shikha, Sengupta, Durba (2024) Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. Journal of Chemical Information and Modeling, 64 (3) 837-850 doi:10.1021/acs.jcim.3c00802
Zhou, Xu, Wei, Zhiqiang, Lu, Hao, He, Jiaqi, Gao, Yuan, Hu, Xiaotong, Wang, Cunji, Dong, Yujie, Liu, Hao (2024) Large-Scale Molecular Dynamics Simulation Based on Heterogeneous Many-Core Architecture. Journal of Chemical Information and Modeling, 64 (3) 851-861 doi:10.1021/acs.jcim.3c01254
Haspel, Nurit, Jang, Hyunbum, Nussinov, Ruth (2024) Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. Journal of Chemical Information and Modeling, 64 (3) 862-873 doi:10.1021/acs.jcim.3c01412
Khamto, Nopawit, Utama, Kraikrit, Boontawee, Panida, Janthong, Atchara, Tatieng, Suriya, Arthan, Supakorn, Choommongkol, Vachira, Sangthong, Padchanee, Yenjai, Chavi, Suree, Nuttee, Meepowpan, Puttinan (2024) Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations. Journal of Chemical Information and Modeling, 64 (3) 874-891 doi:10.1021/acs.jcim.3c01477
Albani, Simone, Costanzi, Elisa, Hoang, Gia Linh, Kuzikov, Maria, Frings, Marcus, Ansari, Narjes, Demitri, Nicola, Nguyen, Toan T., Rizzi, Valerio, Schulz, Jörg B., Bolm, Carsten, Zaliani, Andrea, Carloni, Paolo, Storici, Paola, Rossetti, Giulia (2024) Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. Journal of Chemical Information and Modeling, 64 (3) 892-904 doi:10.1021/acs.jcim.3c01497
Mahdizadeh, Sayyed Jalil, Stier, Michael, Carlesso, Antonio, Lamy, Aurore, Thomas, Melissa, Eriksson, Leif A. (2024) Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase. Journal of Chemical Information and Modeling, 64 (3) 905-917 doi:10.1021/acs.jcim.3c01600
Tolstova, Anna P., Makarov, Alexander A., Adzhubei, Alexei A. (2024) Structure Comparison of Beta Amyloid Peptide Aβ 1–42 Isoforms. Molecular Dynamics Modeling. Journal of Chemical Information and Modeling, 64 (3) 918-932 doi:10.1021/acs.jcim.3c01624
Kang, Christopher, Shoji, Alyson, Chipot, Christophe, Sun, Rui (2024) Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. Journal of Chemical Information and Modeling, 64 (3) 933-943 doi:10.1021/acs.jcim.3c01629
Kaur, Rajwinder, Wetmore, Stacey D. (2024) Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. Journal of Chemical Information and Modeling, 64 (3) 944-959 doi:10.1021/acs.jcim.3c01775
Bekar-Cesaretli, Ayse A., Khan, Omeir, Nguyen, Thu, Kozakov, Dima, Joseph-Mccarthy, Diane, Vajda, Sandor (2024) Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. Journal of Chemical Information and Modeling, 64 (3) 960-973 doi:10.1021/acs.jcim.3c01761
Mei, Yunhao, Shen, Yong (2024) Cation–π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. Journal of Chemical Information and Modeling, 64 (3) 974-982 doi:10.1021/acs.jcim.3c01883
Roy, Anupom, Karttunen, Mikko (2024) A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase. Journal of Chemical Information and Modeling, 64 (3) 983-1003 doi:10.1021/acs.jcim.3c01966
Knight, Ian S., Mailhot, Olivier, Tang, Khanh G., Irwin, John J. (2024) DockOpt: A Tool for Automatic Optimization of Docking Models. Journal of Chemical Information and Modeling, 64 (3) 1004-1016 doi:10.1021/acs.jcim.3c01406
Akhter, Sana, Tang, Zhichao, Wang, Jinan, Haboro, Mercy, Holmstrom, Erik D, Wang, Jingxin, Miao, Yinglong (2024) Mechanism of Ligand Binding to Theophylline RNA Aptamer. Journal of Chemical Information and Modeling, 64 (3) 1017-1029 doi:10.1021/acs.jcim.3c01454
Novakova, Zora, Tehrani, Zahra Aliakbar, Jurok, Radek, Motlova, Lucia, Kutil, Zsofia, Pavlicek, Jiri, Shukla, Shivam, Choy, Cindy J., Havlinova, Barbora, Baranova, Petra, Berkman, Clifford E., Kuchar, Martin, Cerny, Jiri, Barinka, Cyril (2024) Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. Journal of Chemical Information and Modeling, 64 (3) 1030-1042 doi:10.1021/acs.jcim.3c01542
Liu, Zi, Zhang, Chengxin, Zhang, Qidi, Zhang, Yang, Yu, Dong-Jun (2024) TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of Chemical Information and Modeling, 64 (3) 1043-1049 doi:10.1021/acs.jcim.3c01455
Zhang, Jiashuo, Wang, Ruheng, Wei, Leyi (2024) MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. Journal of Chemical Information and Modeling, 64 (3) 1050-1065 doi:10.1021/acs.jcim.3c01471
Guo, Shuang, Liu, Yuwei, Sun, Yue, Zhou, Hanxiao, Gao, Yue, Wang, Peng, Zhi, Hui, Zhang, Yakun, Gan, Jing, Ning, Shangwei (2024) Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer. Journal of Chemical Information and Modeling, 64 (3) 1066-1080 doi:10.1021/acs.jcim.3c01473
Goulard Coderc de Lacam, Emma, Roux, Benoît, Chipot, Christophe (2024) Classifying Protein–Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. Journal of Chemical Information and Modeling, 64 (3) 1081-1091 doi:10.1021/acs.jcim.3c01586
Zhong, Guolun, Deng, Lei (2024) ACPScanner: Prediction of Anticancer Peptides by Integrated Machine Learning Methodologies. Journal of Chemical Information and Modeling, 64 (3) 1092-1104 doi:10.1021/acs.jcim.3c01860
Molani, Farzad, Webb, Simon, Cho, Art E. (2024) Correction to “Combining QM/MM Calculations with Classical Mining Minima to Predict Protein–Ligand Binding Free Energy”. Journal of Chemical Information and Modeling, 64 (3) 1105 doi:10.1021/acs.jcim.3c02002
Sun, Shan, Fushimi, Makoto, Rossetti, Thomas, Kaur, Navpreet, Ferreira, Jacob, Miller, Michael, Quast, Jonathan, van den Heuvel, Joop, Steegborn, Clemens, Levin, Lonny R., Buck, Jochen, Myers, Robert W., Kargman, Stacia, Liverton, Nigel, Meinke, Peter T., Huggins, David J. (2024) Addition to “Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation”. Journal of Chemical Information and Modeling, 64 (3) 1106 doi:10.1021/acs.jcim.4c00068

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