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Journal of Chemical Information and Modeling
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Novel Combination Therapy for Heart Failure: Trimebutine–Methoxsalen Identified through Synergistic Network Virtual Screening and Experimental Validation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Yunyuan Huang, Xin Chen, Jin Yang, Yue Yao, Manjiong Wang, Taotao Lu, Xiao Li, Jiqun Wang, Sicong Qiao, Donglei Shi, Xiaokang Li, Jian Li, Yixiang Xu
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MPNTEXT: An Interactive Platform for Automatically Extracting Metal-Polyphenol Networks and Their Applications from Scientific Literature J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-11 Zihui Huang, Xinyi Li, Andi Li, Yuhang Yang, Liqiang He, Zhiwen Zhang, Siwei Wu, Yang Wang, Shuting Cai, Yan He, Xujie Liu
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Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-10 Tatiana I. Mulashkina, Anna M. Kulakova, Maria G. Khrenova
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IEV2Mol: Molecular Generative Model Considering Protein–Ligand Interaction Energy Vectors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-10 Mami Ozawa, Shogo Nakamura, Nobuaki Yasuo, Masakazu Sekijima
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Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-10 Koichi Handa, Shunta Sasaki, Satoshi Asano, Michiharu Kageyama, Takeshi Iijima, Andreas Bender
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Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-09 Miguel Riopedre-Fernandez, Vojtech Kostal, Tomas Martinek, Hector Martinez-Seara, Denys Biriukov
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All-Atom Membrane Builder via Multiscale Simulation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-09 Siyoung Kim
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DrugSynthMC: An Atom-Based Generation of Drug-like Molecules with Monte Carlo Search J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-09 Milo Roucairol, Alexios Georgiou, Tristan Cazenave, Filippo Prischi, Olivier E. Pardo
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Drug–Target Interactions Prediction at Scale: The Komet Algorithm with the LCIdb Dataset J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-05 Gwenn Guichaoua, Philippe Pinel, Brice Hoffmann, Chloé-Agathe Azencott, Véronique Stoven
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FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-05 Hirotomo Moriwaki, Yusuke Kawashima, Chiduru Watanabe, Kikuko Kamisaka, Yoshio Okiyama, Kaori Fukuzawa, Teruki Honma
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Open-Source Approach to GPU-Accelerated Substructure Search J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-03 Andrew J. Whitehouse, Melchor Sanchez-Martinez, Seyedeh Maryam Salehi, Natalja Kurbatova, Euan Dean
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Sulfoglycodendron Antivirals with Scalable Architectures and Activities J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-04 Francesco Coppola, Roya Jafari, Katherine D. McReynolds, Petr Král
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RBNE-CMI: An Efficient Method for Predicting circRNA-miRNA Interactions via Multiattribute Incomplete Heterogeneous Network Embedding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-04 Chang-Qing Yu, Xin-Fei Wang, Li-Ping Li, Zhu-Hong You, Zhong-Hao Ren, Peng Chu, Feng Guo, Zhen-Yu Wang
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Predicting Small Molecule Binding Nucleotides in RNA Structures Using RNA Surface Topography J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-04 Jiaming Gao, Haoquan Liu, Chen Zhuo, Chengwei Zeng, Yunjie Zhao
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Large Language Models as Molecular Design Engines J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-04 Debjyoti Bhattacharya, Harrison J. Cassady, Michael A. Hickner, Wesley F. Reinhart
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AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-03 Reyes Núñez-Franco, M. Milagros Muriel-Olaya, Gonzalo Jiménez-Osés, Francesca Peccati
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Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-09-03 Hsu-Chun Tsai, James Xu, Zhenyu Guo, Yinhui Yi, Chuan Tian, Xinyu Que, Timothy Giese, Tai-Sung Lee, Darrin M. York, Abir Ganguly, Albert Pan
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Rotation and Self-Assembly Driving NLRP3 Activation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-27 Haochen Xu, Zhonghuai Hou, Rongbin Zhou, Jie-Lou Liao
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Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR) J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-29 Minos-Timotheos Matsoukas, Tarryn Radomsky, Vasilis Panagiotopoulos, Robin du Preez, Michail Papadourakis, Konstantinos Tsianakas, Robert P Millar, Ross C Anderson, Georgios A Spyroulias, Claire L Newton
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Multitask Learning on Graph Convolutional Residual Neural Networks for Screening of Multitarget Anticancer Compounds J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-28 Thanh-Hoang Nguyen-Vo, Trang T. T. Do, Binh P. Nguyen
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Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-28 Vishva Saravanan R, Soham Choudhuri, Bhaswar Ghosh
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Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-28 Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao, Guodong Hu
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Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-27 Xuezhi Xie, Pedro A. Valiente, Jin Sub Lee, Jisun Kim, Philip M. Kim
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Synergistic Antimicrobial Mechanism of the Ultrashort Antimicrobial Peptide R3W4V with a Tadpole-like Conformation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-26 Zanxia Cao, Zhihong Shi, Mingqiong Tong, Dongying Yang, Lei Liu
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SmartCADD: AI-QM Empowered Drug Discovery Platform with Explainability J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-23 Ayesh Madushanka, Eli Laird, Corey Clark, Elfi Kraka
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Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-28 R. Beccaria, A. Lazzeri, G. Tiana
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Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH-1 J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-23 Carlo Bigiotti, Elisa Bianconi, Luana Ruta, Silvia Grottelli, Alice Coletti, Mirco Dindo, Andrea Carotti, Barbara Cellini, Antonio Macchiarulo
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Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-22 Lingling Wang, Shu Li, Sutong Xiang, Huanxiang Liu, Huiyong Sun
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Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-21 Cristian Orgaz, Andrés Sánchez-Ruiz, Gonzalo Colmenarejo
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Predicting the Dynamic Interaction of Intrinsically Disordered Proteins J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-20 Yuchuan Zheng, Qixiu Li, Maria I. Freiberger, Haoyu Song, Guorong Hu, Moxin Zhang, Ruoxu Gu, Jingyuan Li
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Characterization of a Novel Monoclonal Antibody with High Affinity and Specificity against Aflatoxins: A Discovery from Rosetta Antibody-Ligand Computational Simulation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-19 Changrui Xing, Guanglei Li, Xin Zheng, Peng Li, Jian Yuan, Wenjing Yan
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Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers” J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-19 Eleftherios Christofi, Petra Bačová, Vagelis A. Harmandaris
Regarding our original paper, concerning the actual flexibility of the PDLA and consequently the values of the internal distances presented in Figures 11, 13, and 15, it is important to note that the same force field parameters have been used for both l- and d-monomers; i.e., these two structures differ only in the spatial position of the hydrogen in the monomer. More specifically, according to the
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RLSynC: Offline–Online Reinforcement Learning for Synthon Completion J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-18 Frazier N. Baker, Ziqi Chen, Daniel Adu-Ampratwum, Xia Ning
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Mapping of the Lipid-Binding Regions of the Antifungal Protein NFAP2 by Exploiting Model Membranes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-16 Olivér Pavela, Tünde Juhász, Liliána Tóth, András Czajlik, Gyula Batta, László Galgóczy, Tamás Beke-Somfai
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Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-16 Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
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pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-16 Carlos A. V. Barreto, João N. M. Vitorino, Pedro B.P.S. Reis, Miguel Machuqueiro, Irina S. Moreira
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Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-15 Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky
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EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-12 Ganna Gryn’ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth Merz, Jr.
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Quantum Chemical and Biological Insights into Redox Activity of Metallacarborane Complexes in Cancer Cells J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-14 Katarzyna Bednarska-Szczepaniak, Krzysztof Hałagan, Marzena Szwed, Ewelina Przelazły, Zbigniew J. Leśnikowski
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Transformers for Molecular Property Prediction: Lessons Learned from the Past Five Years J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-13 Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer
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Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-13 Wilfred F. van Gunsteren, Chris Oostenbrink
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A Multi-Angle Approach to Predict Peptide-GPCR Complexes: The N/OFQ-NOP System as a Successful AlphaFold Application Case Study J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-13 Antonella Ciancetta, Davide Malfacini, Matteo Gozzi, Erika Marzola, Riccardo Camilotto, Girolamo Calò, Remo Guerrini
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Balancing Molecular Size, Activity, Permeability, and Other Properties: Drug Candidates in the Context of Their Chemical Structure Optimization J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-13 Maximilian Beckers, Finton Sirockin, Nikolas Fechner, Nikolaus Stiefl
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MGNDTI: A Drug-Target Interaction Prediction Framework Based on Multimodal Representation Learning and the Gating Mechanism J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-13 Lihong Peng, Xin Liu, Min Chen, Wen Liao, Jiale Mao, Liqian Zhou
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MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-12 Muhammad Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, Van The Le, Yu-Yen Ou
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Enthalpic Classification of Water Molecules in Target–Ligand Binding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-12 Viktor Szél, Balázs Zoltán Zsidó, Csaba Hetényi
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NJmat: Data-Driven Machine Learning Interface to Accelerate Material Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-12 Yiru Huang, Lei Zhang, Hangyuan Deng, Junfei Mao
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The Block Copolymer Phase Behavior Database J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-10 Nathan J. Rebello, Akash Arora, Hidenobu Mochigase, Tzyy-Shyang Lin, Jiale Shi, Debra J. Audus, Eric S. Muckley, Ardiana Osmani, Bradley D. Olsen
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Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-09 Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov
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Assessing Aquatic Baseline Toxicity of Plastic-Associated Chemicals: Development and Validation of the Target Plastic Model J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-09 Deedar Nabi, Aaron J. Beck, Eric P. Achterberg
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Glypred: Lysine Glycation Site Prediction via CCU–LightGBM–BiLSTM Framework with Multi-Head Attention Mechanism J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-09 Yun Zuo, Bangyi Zhang, Yinkang Dong, Wenying He, Yue Bi, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
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ncRNA Coding Potential Prediction Using BiLSTM and Transformer Encoder-Based Model J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-09 Jingpu Zhang, Hao Lu, Ying Jiang, Yuanyuan Ma, Lei Deng
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DDSBC: A Stacking Ensemble Classifier-Based Approach for Breast Cancer Drug-Pair Cell Synergy Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 Aamir Mehmood, Aman Chandra Kaushik, Dong-Qing Wei
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lwreg: A Lightweight System for Chemical Registration and Data Storage J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 Gregory A. Landrum, Jessica Braun, Paul Katzberger, Marc T. Lehner, Sereina Riniker
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RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 Qirui Deng, Zhe Wang, Sutong Xiang, Qinghua Wang, Yifei Liu, Tingjun Hou, Huiyong Sun
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Epithelial–Mesenchymal Transition Related Score Functions as a Predictive Tool for Immunotherapy and Candidate Drugs in Glioma J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 Xiaojun Fu, Changyuan Ren, Kaining Dai, Ming Ren, Changxiang Yan
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High-Throughput Screening and Prediction of Nucleophilicity of Amines Using Machine Learning and DFT Calculations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 Xu Li, Haoliang Zhong, Haoyu Yang, Lin Li, Qingji Wang
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Evaluation of AlphaFold 3’s Protein–Protein Complexes for Predicting Binding Free Energy Changes upon Mutation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-08 JunJie Wee, Guo-Wei Wei
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Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-07 Ping Xuan, Wei Wang, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Tiangang Zhang
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Machine-Learning Prediction of Curie Temperature from Chemical Compositions of Ferromagnetic Materials J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-08-07 Son Gyo Jung, Guwon Jung, Jacqueline M. Cole
更新日期：2024-09-11
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