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Cysteine Radical and Glutamate Collaboratively Enable C–H Bond Activation and C–N Bond Cleavage in a Glycyl Radical Enzyme HplG J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-14 Wen-Hao Deng, Rong-Zhen Liao
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Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-14 Fengjuan Huang, Jiahui Huang, Jiajia Yan, Yuying Liu, Jiangfang Lian, Qinxue Sun, Feng Ding, Yunxiang Sun
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DPMGCDA: Deciphering circRNA–Drug Sensitivity Associations with Dual Perspective Learning and Path-Masked Graph Autoencoder J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-14 Yue Luo, Lei Deng
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In SilicoDesign and Synthesis of Antifungal Peptides Guided by Quantitative Antifungal Activity J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-14 Jin Zhang, Xinhao Sun, Hongwei Zhao, Xu Zhou, Yiling Zhang, Feng Xie, Boyan Li, Guo Guo
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AIGO-DTI: Predicting Drug–Target Interactions Based on Improved Drug Properties Combined with Adaptive Iterative Algorithms J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-14 Sizhe Zhang, Xuecong Tian, Chen Chen, Ying Su, Wanhua Huang, Xiaoyi Lv, Cheng Chen, Hongyi Li
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Improving Anticancer Drug Selection and Prioritization via Neural Learning to Rank J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-13 Vishal Dey, Xia Ning
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Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-13 Greneter Cordoves-Delgado, César R. García-Jacas
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Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-13 Payam Kelich, Jaquesta Adams, Sanghwa Jeong, Nicole Navarro, Markita P. Landry, Lela Vuković
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Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-13 Hosein Fooladi, Steffen Hirte, Johannes Kirchmair
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CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-13 Rongpei Gou, Jingyi Yang, Menghan Guo, Yingjun Chen, Weiwei Xue
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MulTFBS: A Spatial-Temporal Network with Multichannels for Predicting Transcription Factor Binding Sites J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-11 Jujuan Zhuang, Xinru Huang, Shuhan Liu, Wanquan Gao, Rui Su, Kexin Feng
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Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-11 Mateusz Rzycki, Dominik Drabik
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PharmaCore: The Automatic Generation of 3D Structure-Based Pharmacophore Models from Protein/Ligand Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-10 Simona De Vita, Ester Colarusso, Maria Giovanna Chini, Giuseppe Bifulco, Gianluigi Lauro
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Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-10 Zishuo Cheng, Mahesh Aitha, Caitlyn A. Thomas, Aidan Sturgill, Mitch Fairweather, Amy Hu, Christopher R. Bethel, Dann D. Rivera, Patricia Dranchak, Pei W. Thomas, Han Li, Qi Feng, Kaicheng Tao, Minshuai Song, Na Sun, Shuo Wang, Surendra Bikram Silwal, Richard C. Page, Walt Fast, Robert A. Bonomo, Maria Weese, Waldyn Martinez, James Inglese, Michael W. Crowder
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Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-10 Farzin Sohraby, Ariane Nunes-Alves
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FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-09 Yueqing Zhang, Zhihan Zhang, Dongliang Ke, Xiaolin Pan, Xingyu Wang, Xudong Xiao, Changge Ji
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Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-09 Ting Qi, Ying Zhou, Yuqi Sheng, Zhihui Li, Yuwei Yang, Quanjun Liu, Qinyu Ge
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Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-08 Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks, III
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Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein–Ligand Binding and Competitive Binding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-08 Yu Du
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Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-08 Yazdan Maghsoud, Arkanil Roy, Emmett M. Leddin, G. Andrés Cisneros
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HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-06 Ning Cheng, Li Wang, Yiping Liu, Bosheng Song, Changsong Ding
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Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human β-Tubulin Isotypes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-05 Sonia Kumari, Masilamani Elizabeth Sobhia
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Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-07 Rafael G. Viegas, Ingrid B. S. Martins, Vitor B. P. Leite
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Exploring Bitter and Sweet: The Application of Large Language Models in Molecular Taste Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-07 Renxiu Song, Kaifeng Liu, Qizheng He, Fei He, Weiwei Han
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Correction to “Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay” J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-07 Jun Zhao, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du
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Leveraging Language Model Multitasking To Predict C–H Borylation Selectivity J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-06 Ruslan Kotlyarov, Konstantinos Papachristos, Geoffrey P. F. Wood, Jonathan M. Goodman
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MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-06 Bao-Ming Feng, Yuan-Yuan Zhang, Xiao-Chen Zhou, Jin-Long Wang, Yin-Fei Feng
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Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-06 Romain Launay, Sophie-Carole Chobert, Sophie S. Abby, Fabien Pierrel, Isabelle André, Jérémy Esque
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Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-06 Juan S. Grassano, Ignacio Pickering, Adrian E. Roitberg, Mariano C. González Lebrero, Dario A. Estrin, Jonathan A. Semelak
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Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-04 José Luis Velázquez-Libera, Julio Caballero, Jans Alzate-Morales, J. Javier Ruiz-Pernía, Iñaki Tuñón
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Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-04 Mehdi Sahihi, Pierre Fayon, Lionel Nauton, Florent Goujon, Julien Devémy, Alain Dequidt, Patrice Hauret, Patrice Malfreyt
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Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood–Brain Barrier Permeability Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-03 Vinay Kumar, Arkaprava Banerjee, Kunal Roy
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Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-03 Sunita Muduli, Soumyajit Karmakar, Sabyashachi Mishra
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SAF: Smart Aggregation Framework for Revealing Atoms Importance Rank and Improving Prediction Rates in Drug Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-02 Ronen Taub, Yonatan Savir
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Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-05-02 Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj
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SDDSynergy: Learning Important Molecular Substructures for Explainable Anticancer Drug Synergy Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-30 Yunjiong Liu, Peiliang Zhang, Chao Che, Ziqi Wei
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DszA Catalyzes C–S Bond Cleavage through N5–Hydroperoxyl Formation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-29 Pedro Ferreira, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria J. Ramos, Pedro A. Fernandes
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Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-30 Yu Zhu, Jing Gu, Zhuoran Zhao, A. W. Edith Chan, Maria F. Mojica, Andrea M. Hujer, Robert A. Bonomo, Shozeb Haider
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Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-30 Moritz Walter, Samuel J. Webb, Valerie J. Gillet
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Machine Learning-Based Prediction of Reduction Potentials for PtIV Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-29 V. Vigna, T. F. G. G. Cova, S. C. C. Nunes, A. A. C. C. Pais, E. Sicilia
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Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Ying Zheng, Nianhang Chen, Zhongju Ji, Qiongyu Ye, Pingping Huang, Xiaodie Chen, Guanghong Cui, Lixin Duan, Fan Zhang
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MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-27 Yu Pang, Yihao Chen, Mujie Lin, Yanhong Zhang, Jiquan Zhang, Ling Wang
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Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Carlos Sequeiros-Borja, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix J. Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky
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Enhancing Coarse-Grained Models through Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz, Jr.
Computer simulations, particularly molecular dynamics (MD) simulations, are effective tools for studying microscopic and dynamic details of complex systems governing various physicochemical and biological processes. Recent advancements in computer hardware and algorithms have significantly improved the efficiency of MD methods and expanded their applicability to the treatment of large macromolecular
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Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi
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COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-26 Maksim Kuznetsov, Fedor Ryabov, Roman Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alex Aliper, Daniil Polykovskiy
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dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-25 Haopeng Ai, Deyin Wu, Huihao Zhou, Jun Xu, Qiong Gu
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DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-24 Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov
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FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-23 Pieter B. Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M. Kaiser
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Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-23 Lina Zhao, Yanjiao Wang, Yi Zhang, Hao Chen, Fude Sun
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Early Aggregation Mechanism of SOD128–38 Based on Force Field Parameter of 5-Cyano-Tryptophan J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-23 Mueed Ur Rahman, Saira Bano, Xiaokun Hong, Ruo-Xu Gu, Hai-Feng Chen
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DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Tzu-Hsien Yang
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Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Paige E. Bowling, Saswata Dasgupta, John M. Herbert
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FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song
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ORDerly: Data Sets and Benchmarks for Chemical Reaction Data J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-22 Daniel S. Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C. Felton, Alexei A. Lapkin
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Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-20 Hajime Shimakawa, Akiko Kumada, Masahiro Sato
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Development of Novel Methods for QSAR Modeling by Machine Learning Repeatedly: A Case Study on Drug Distribution to Each Tissue J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-19 Koichi Handa, Saki Yoshimura, Michiharu Kageyama, Takeshi Iijima
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On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-19 Stefan Boresch
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Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-18 Kriti Shukla, Kelvin Idanwekhai, Martin Naradikian, Stephanie Ting, Stephen P. Schoenberger, Elizabeth Brunk
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Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-18 Sankar Maity, Somdev Pahari, Santanu Santra, Madhurima Jana