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In Silico Prediction of Oral Acute Rodent Toxicity Using Consensus Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-18 Sebastian Schieferdecker, Florian Rottach, Esther Vock
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Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-18 Teng-Zhi Long, De-Jun Jiang, Shao-Hua Shi, You-Chao Deng, Wen-Xuan Wang, Dong-Sheng Cao
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Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-15 Yu Zou, Lulu Guan, Jingwang Tan, Bote Qi, Yunxiang Sun, Fengjuan Huang, Qingwen Zhang
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Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-15 Yuheng Ding, Bo Qiang, Qixuan Chen, Yiqiao Liu, Liangren Zhang, Zhenming Liu
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Recent Advances in Automated Structure-Based De Novo Drug Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Yidan Tang, Rocco Moretti, Jens Meiler
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RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-15 Babak A. Mahjour, Connor W. Coley
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Physics-Informed Generative Model for Drug-like Molecule Conformers J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 David C. Williams, Neil Inala
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HBCalculator: A Tool for Hydrogen Bond Distribution Calculations in Molecular Dynamics Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Yulei Wang, Yuxiang Wang
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Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein–Cyclic Peptide Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
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Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
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Enhanced Calculation of Property Distributions in Chemical Fragment Spaces J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-11 Justin Lübbers, Uta Lessel, Matthias Rarey
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PMechDB: A Public Database of Elementary Polar Reaction Steps J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Mohammadamin Tavakoli, Ryan J. Miller, Mirana Claire Angel, Michael A. Pfeiffer, Eugene S. Gutman, Aaron D. Mood, David Van Vranken, Pierre Baldi
Most online chemical reaction databases are not publicly accessible or are fully downloadable. These databases tend to contain reactions in noncanonicalized formats and often lack comprehensive information regarding reaction pathways, intermediates, and byproducts. Within the few publicly available databases, reactions are typically stored in the form of unbalanced, overall transformations with minimal
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EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-14 Javad Tayebi, Bagher BabaAli
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LinChemIn: Route Arithmetic─Operations on Digital Synthetic Routes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-13 Marta Pasquini, Marco Stenta
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The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-13 Matic Broz, Chris Oostenbrink, Urban Bren
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Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 Mpro Inhibitors from Large Chemical Libraries J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-12 Angel J. Ruiz-Moreno, Raziel Cedillo-González, Luis Cordova-Bahena, Zhiqiang An, José L. Medina-Franco, Marco A. Velasco-Velázquez
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Database-Driven Identification of Structurally Similar Protein-Protein Interfaces J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-12 Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
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Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-12 Derek P. Metcalf, Zachary L. Glick, Andrea Bortolato, Andy Jiang, Daniel L. Cheney, C. David Sherrill
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Implementation of IFPTML Computational Models in Drug Discovery Against Flaviviridae Family J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-11 Yendrek Velásquez-López, Andrea Ruiz-Escudero, Sonia Arrasate, Humberto González-Díaz
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Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-09 Amit Kumar, Harish Vashisth
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Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-07 Zachary Smith, Michael Strobel, Bodhi P. Vani, Pratyush Tiwary
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Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-05 Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang
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Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-08 Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda
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Coarse-Grained Crystal Graph Neural Networks for Reticular Materials Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-08 Vadim Korolev, Artem Mitrofanov
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Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-08 Farag E. S. Mosa, Sara AlRawashdeh, Ayman O. S. El-Kadi, Khaled Barakat
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Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita–Baylis–Hillman Reaction: Why Is Enzyme Design so Difficult? J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-07 Sree Ganesh Balasubramani, Kseniia Korchagina, Steven Schwartz
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Determinants of Neutral Antagonism and Inverse Agonism in the β2-Adrenergic Receptor J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-06 Jacqueline C. Calderón, Passainte Ibrahim, Dorothea Gobbo, Francesco Luigi Gervasio, Timothy Clark
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DeePNAP: A Deep Learning Method to Predict Protein–Nucleic Acid Binding Affinity from Their Sequences J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-08 Uddeshya Pandey, Sasi M. Behara, Siddhant Sharma, Rachit S. Patil, Souparnika Nambiar, Debasish Koner, Hussain Bhukya
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Probe Substrate Dependencies in CYP3A4 Allosteric Inhibition: A Novel Molecular Mechanism Involving F–F′ Loop Perturbations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-08 Wan Wei, Lloyd Wei Tat Tang, Ravi Kumar Verma, Hao Fan, Eric Chun Yong Chan
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Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-07 Kuo Hao Lee, Lei Shi
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Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6 J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-07 Szymon Zdybel, Anita Sosnowska, Dominika Kowalska, Julia Sommer, Beate Conrady, Patrick Mester, Maciej Gromelski, Tomasz Puzyn
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Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-06 Rohan Gorantla, Alžbeta Kubincová, Benjamin Suutari, Benjamin P. Cossins, Antonia S. J. S. Mey
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Large-Scale Pretraining Improves Sample Efficiency of Active Learning-Based Virtual Screening J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-05 Zhonglin Cao, Simone Sciabola, Ye Wang
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Predicting Cardiotoxicity of Molecules Using Attention-Based Graph Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-04 Tuan Vinh, Loc Nguyen, Quang H. Trinh, Thanh-Hoang Nguyen-Vo, Binh P. Nguyen
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Exploiting Vector Pattern Diversity of Molecular Scaffolds for Cheminformatics Tasks in Drug Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-04 Daniela Dolciami, Robert M. Ziolek, Daniel W. Davies, Michael Carter, N. Yi Mok, Richard Sherhod
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Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-04 Philipe Oliveira Fernandes, Anna Letícia Teotonio Dias, Valtair Severino dos Santos Júnior, Mateus Sá Magalhães Serafim, Yamara Viana Sousa, Gustavo Claro Monteiro, Isabel Duarte Coutinho, Marilia Valli, Marina Mol Sena Andrade Verzola, Flaviano Melo Ottoni, Rodrigo Maia de Pádua, Fernando Bombarda Oda, André Gonzaga dos Santos, Adriano Defini Andricopulo, Vanderlan da Silva Bolzani, Bruno Eduardo
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Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer’s Disease J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-01 Shawn C. C. Hsueh, Mark Nijland, Adekunle Aina, Steven S. Plotkin
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Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-29 Floriane Eshak, Léo Pion, Pauline Scholler, Damien Nevoltris, Patrick Chames, Philippe Rondard, Jean-Philippe Pin, Francine C. Acher, Anne Goupil-Lamy
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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 : 2024-03-01 Eleftherios Christofi, Petra Bačová, Vagelis A. Harmandaris
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On Inactivation of the Coronavirus Main Protease J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-29 Hong Ha Nguyen, Jim Tufts, David D. L. Minh
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Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-29 Son Gyo Jung, Guwon Jung, Jacqueline M. Cole
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APE-Gen2.0: Expanding Rapid Class I Peptide–Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-28 Romanos Fasoulis, Mauricio M. Rigo, Gregory Lizée, Dinler A. Antunes, Lydia E. Kavraki
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ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-28 Jochem Nelen, Miguel Carmena-Bargueño, Carlos Martínez-Cortés, Alejandro Rodríguez-Martínez, José Manuel Villalgordo-Soto, Horacio Pérez-Sánchez
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Pliability in the m6A-Binding Region Extends Druggability of YTH Domains J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-28 Giulia Cazzanelli, Andrea Dalle Vedove, Giovanni Spagnolli, Luca Terruzzi, Enrica Colasurdo, Alberto Boldrini, Alexandros Patsilinakos, Mattia Sturlese, Alessandro Grottesi, Emiliano Biasini, Alessandro Provenzani, Alessandro Quattrone, Graziano Lolli
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PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-25 Petrina Kamya, Ivan V. Ozerov, Frank W. Pun, Kyle Tretina, Tatyana Fokina, Shan Chen, Vladimir Naumov, Xi Long, Sha Lin, Mikhail Korzinkin, Daniil Polykovskiy, Alex Aliper, Feng Ren, Alex Zhavoronkov
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DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-27 Marjolein T. Oostrom, Sean M. Colby, Thomas O. Metz
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MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-27 Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng
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Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-27 Kaylen R. Meeks, Juan Ji, Mykola V. Protopopov, Olga O. Tarkhanova, Yurii S. Moroz, John J. Tanner
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Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-27 Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino
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Benchmarking Water Models in Molecular Dynamics of Protein–Glycosaminoglycan Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-27 Sebastian Anila, Sergey A. Samsonov
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Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-26 Dávid Zajaček, Adriána Dunárová, Lukas Bucinsky, Marek Štekláč
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AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-26 Zuojun Yang, Yuhan Wu, Hao Liu, Li He, Xiaoyuan Deng
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Correction to “De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder” J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-26 Nutaya Pravalphruekul, Maytus Piriyajitakonkij, Phond Phunchongharn, Supanida Piyayotai
Listed below are the needed corrections and additions for the misplaced variables and missing descriptions. These descriptive changes are made to accurately detail the workings of the model; they do not at all affect the results and conclusions drawn. We offer our thanks to Dr. Nat Dilokthanakul for pointing out the inaccurate and absent elements. On page 4002, the variables should be written as follows
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Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-22 Niccolo Alberto Elia Venanzi, Andrea Basciu, Attilio Vittorio Vargiu, Alexandros Kiparissides, Paul A. Dalby, Duygu Dikicioglu
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Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-23 Gregory A. Landrum, Sereina Riniker
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Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion’s Polarizability and Molecular Mass with Limited Data J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-23 Pattipong Wisanpitayakorn, Sitanan Sartyoungkul, Alongkorn Kurilung, Yongyut Sirivatanauksorn, Wonnop Visessanguan, Nuankanya Sathirapongsasuti, Sakda Khoomrung
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MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-22 Fernando Garcia-Escobar, Toshiaki Taniike, Keisuke Takahashi
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Storing Images in DNA via base128 Encoding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-22 Kun Wang, Ben Cao, Tao Ma, Yunzhu Zhao, Yanfen Zheng, Bin Wang, Shihua Zhou, Qiang Zhang
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Machine Learning for Sequence and Structure-Based Protein–Ligand Interaction Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-22 Yunjiang Zhang, Shuyuan Li, Kong Meng, Shaorui Sun
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Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein–Ligand Interactions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-02-21 Xiaohe Xu, Weijie Han, Xiangzhen Ning, Chengdong Zang, Chengcheng Xu, Chen Zeng, Chengtao Pu, Yanmin Zhang, Yadong Chen, Haichun Liu