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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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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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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
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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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Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang
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Protein Engineering with Lightweight Graph Denoising Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Bingxin Zhou, Lirong Zheng, Banghao Wu, Yang Tan, Outongyi Lv, Kai Yi, Guisheng Fan, Liang Hong
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Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-17 Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiří Šponer, Petr Stadlbauer
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AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R. Houston
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Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Marzieh Saeedimasine, Roja Rahmani, Alexander P. Lyubartsev
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Understanding the Modulatory Role of E2012 on the γ-Secretase–Substrate Interaction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-16 Dulce C. Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, Laura Dominguez
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Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-15 Otávio L. Santana, Daniel G. Silva, Sidney R. Santana
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Intramolecular and Water Mediated Tautomerism of Solvated Glycine J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-15 Pengchao Zhang, Axel Tosello Gardini, Xuefei Xu, Michele Parrinello
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Leveraging Bidirectional Nature of Allostery To Inhibit Protein–Protein Interactions (PPIs): A Case Study of PCSK9–LDLR Interaction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-14 Krishnendu Sinha, Ipsita Basu, Zacharia Shah, Salim Shah, Suman Chakrabarty
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Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-12 Dhiman Ray, Sudip Das, Umberto Raucci
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Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-11 Riya Samanta, Xinhao Zhuang, Kristen M. Varney, David J. Weber, Silvina Matysiak
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Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-11 Annie M. Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Mikhail Kabeshov, Rocío Mercado, Samuel Genheden
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Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-11 Luis J. Walter, Patrick K. Quoika, Martin Zacharias
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Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes? J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-10 Shreya Bhattacharya, Priyadarshi Satpati
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Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-10 Satyabrata Majumder, Giuseppe Deganutti, Ludovico Pipitò, Dwaipayan Chaudhuri, Joyeeta Datta, Kalyan Giri
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Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-10 David Ferro-Costas, Pedro A. Sánchez-Murcia, Antonio Fernández-Ramos
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Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-09 Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li
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Using Three-Dimensional Information to Predict and Interpret the Facial Selectivities of Nucleophilic Additions to Cyclic Ketones J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-09 Daimon Sakaguchi, Hiroaki Gotoh
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High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Filipe E. P. Rodrigues, Tamis Darbre, Miguel Machuqueiro
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ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Lianci Tao, Tong Zhou, Zhixiang Wu, Fangrui Hu, Shuang Yang, Xiaotian Kong, Chunhua Li
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Modeling Zinc Complexes Using Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Hongni Jin, Kenneth M. Merz, Jr.
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DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Jiamin Chang, Xiaoyu Fan, Boxue Tian
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Editorial: Machine Learning in Bio-cheminformatics J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Kenneth M. Merz, Guo-Wei Wei, Feng Zhu
In recent years, the application of machine learning (ML), including deep learning (DL), has experienced exponential growth, which has promoted data-driven discovery in diverse fields, particularly in bioinformatics and cheminformatics. ML identifies the hidden patterns from large amounts of biological/chemical data to make predictions or decisions. Specifically, ML-based frameworks have been successfully
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Applications of Free-Energy Calculations to Biomolecular Processes. A Collection J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-08 Zoe Cournia, Christophe Chipot
This Editorial is jointly published in The Journal of Physical Chemistry B and Journal of Chemical Information and Modeling. This article references 22 other publications. This article has not yet been cited by other publications. This article references 22 other publications.
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Addition to “Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model” J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-05 Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud
In our recent publication, (1) we introduced a series of Force Fields (FFs) for the actinyl molecular cations using the 12-6-4 model. After publication, we realized that certain parameters were missing in the paper. These parameters are essential for reproducing our results and for using the new actinyl force fields. First, the Lennard-Jones parameters for the oxygen atoms in the actinyl cations were
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Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-03 Debashree Chakraborty, Omkar Singh, Divya Parameswaran
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Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-02 Ander Francisco Pereira, Leandro Martínez
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Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-04 Maxwell C. Venetos, Masha Elkin, Connor Delaney, John F. Hartwig, Kristin A. Persson
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ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-04 Xiangwen Wang, Derek Quinn, Thomas S. Moody, Meilan Huang
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Hodge Decomposition of Single-Cell RNA Velocity J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-04 Zhe Su, Yiying Tong, Guo-Wei Wei
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Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-02 Jianing Fan, Shaohua Shi, Hong Xiang, Li Fu, Yanjing Duan, Dongsheng Cao, Hongwei Lu
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Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-02 Tengyu Xie, Jing Huang
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MolProphet: A One-Stop, General Purpose, and AI-Based Platform for the Early Stages of Drug Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-04-02 Keda Yang, Zewen Xie, Zhen Li, Xiaoliang Qian, Nannan Sun, Tao He, Zuodong Xu, Jing Jiang, Qi Mei, Jie Wang, Shugang Qu, Xiaoling Xu, Chaoxiang Chen, Bin Ju
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PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-30 Ramil Nugmanov
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pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular Approach J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-30 Felipe L. Oliveira, Pierre M. Esteves
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Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-28 Luis Macaya, Duván González, Esteban Vöhringer-Martinez
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Computational Investigation of the Covalent Inhibition Mechanism of Bruton’s Tyrosine Kinase by Ibrutinib J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-28 Angela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoît Roux
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Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-28 Hongyan Chen, Dongxue Yan, Jie Sun, Meng Zhou
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Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-27 Ru-De Lin, Xiu Xing, Yuan Yu, Wen-Dian Li, Dan-Dan Chang, Fei-Yan Tao, Na Wang
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How Beneficial Is Pretraining on a Narrow Domain-Specific Corpus for Information Extraction about Photocatalytic Water Splitting? J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-27 Taketomo Isazawa, Jacqueline M. Cole
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Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-27 Rodrigo A. Cormanich, Gabriel D. da Silva
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Predicting the Activity of Unidentified Chemicals in Complementary Bioassays from the HRMS Data to Pinpoint Potential Endocrine Disruptors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-24 Ida Rahu, Meelis Kull, Anneli Kruve
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HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-29 Andreas Zamanos, George Ioannakis, Ioannis Z. Emiris
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HSQC Spectra Simulation and Matching for Molecular Identification J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-27 Martin Priessner, Richard J. Lewis, Magnus J. Johansson, Jonathan M. Goodman, Jon Paul Janet, Anna Tomberg
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Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-27 Nicolas Chéron
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DeepKa Web Server: High-Throughput Protein pKa Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-26 Zhitao Cai, Hao Peng, Shuo Sun, Jiahao He, Fangfang Luo, Yandong Huang
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From NMR to AI: Designing a Novel Chemical Representation to Enhance Machine Learning Predictions of Physicochemical Properties J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-26 Arkadiusz Leniak, Wojciech Pietruś, Rafał Kurczab
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Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-26 Xuefeng Bai, Yabo Xie, Xin Zhang, Honggui Han, Jian-Rong Li
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Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-26 Mustafa Kemal Ozalp, Patricia A. Vignaux, Ana C. Puhl, Thomas R. Lane, Fabio Urbina, Sean Ekins
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Correlation of the Molecular Cross-Sectional Area of Organic Monofunctional Compounds with Topological Descriptors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-25 Didier Desmecht, Vincent Dubois
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Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-25 Akie Kowaguchi, Paul E. Brumby, Kenji Yasuoka
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Learning Association Characteristics by Dynamic Hypergraph and Gated Convolution Enhanced Pairwise Attributes for Prediction of Disease-Related lncRNAs J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-24 Ping Xuan, Siyuan Lu, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Tiangang Zhang
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ProInterVal: Validation of Protein–Protein Interfaces through Learned Interface Representations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-25 Damla Ovek, Ozlem Keskin, Attila Gursoy
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Empowering Graph Neural Networks with Block-Based Dual Adaptive Deep Adjustment for Drug Resistance-Related NcRNA Discovery J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-24 Yi Zhang, Xuanzhao Li
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Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-24 Lorenza Pirona, Federico Ballabio, Mercedes Alfonso-Prieto, Riccardo Capelli
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Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network J. Chem. Inf. Model. (IF 5.6) Pub Date : 2024-03-23 Zhihao Gu, Yong Yan, Hanwen Liu, Di Wu, Hequan Yao, Kejiang Lin, Xuanyi Li