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Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-07 Rubina, Syed Tarique Moin
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HOMA Index Establishes Similarity to a Reference Molecule J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Jan Cz. Dobrowolski, Sławomir Ostrowski
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Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Katarzyna Kapuścińska, Zofia Dukała, Mekhola Doha, Eman Ansari, Jimin Wang, Gary W. Brudvig, Bernand Brooks, Muhamed Amin
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Transferring a Molecular Foundation Model for Polymer Property Predictions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Pei Zhang, Logan Kearney, Debsindhu Bhowmik, Zachary Fox, Amit K. Naskar, John Gounley
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LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Anthony T. Bogetti, Jeremy M. G. Leung, Lillian T. Chong
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BrainPepPass: A Framework Based on Supervised Dimensionality Reduction for Predicting Blood-Brain Barrier-Penetrating Peptides J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Ewerton Cristhian Lima de Oliveira, Hannah Hirmz, Evelien Wynendaele, Juliana Auzier Seixas Feio, Igor Matheus Souza Moreira, Kauê Santana da Costa, Anderson H. Lima, Bart De Spiegeleer, Claudomiro de Souza de Sales Júnior
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Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang, Tzong-Yi Lee
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Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-06 Huaxin Zhou, Haohao Fu, Xueguang Shao, Wensheng Cai
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Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Aharon Gomez, Tobias J. Erb, Helmut Grubmüller, Esteban Vöhringer-Martinez
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Scipion-Chem: An Open Platform for Virtual Drug Screening J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-05 Daniel Del Hoyo, Martin Salinas, Alba Lomas, Eugenia Ulzurrun, Nuria E. Campillo, Carlos Oscar Sorzano
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Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-05 Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, Toan T. Nguyen, Valerio Rizzi, Jörg B. Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti
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Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-05 Julian M. Delgado, Péter R. Nagy, Sameer Varma
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Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-05 Anjana V. Mathath, Bratin Kumar Das, Debashree Chakraborty
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Two-Step Covalent Docking with Attracting Cavities J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Mathilde Goullieux, Vincent Zoete, Ute F. Röhrig
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Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Aaron G. Garrison, Javier Heras-Domingo, John R. Kitchin, Gabriel dos Passos Gomes, Zachary W. Ulissi, Samuel M. Blau
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Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Zhipeng Wu, Yejian Wu, Cheng Zhu, Xinyi Wu, Silong Zhai, Xinqiao Wang, Zhihao Su, Hongliang Duan
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MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Matthijs L. A. Hakkennes, Francesco Buda, Sylvestre Bonnet
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Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-04 Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai-Bin Luo, Zhe Li
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Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4 J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-01 Dongxiao Yue, Hajime Hirao
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A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-12-01 Heqi Sun, Jianmin Wang, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong, Dong-Qing Wei
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Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-28 Shide Liang, Chi Zhang, Mingfu Zhu
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Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-30 Miroslava Nedyalkova, Giovanni Russo, Philip Loche, Marco Lattuada
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VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-27 Robin Skånberg, Ingrid Hotz, Anders Ynnerman, Mathieu Linares
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Molecular Insights into the MLCK Activation by CaM J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-28 Xuan Fang, Vladimir Bogdanov, Jonathan P. Davis, Peter M. Kekenes-Huskey
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PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-28 Yuko Tsuchiya, Tomoki Yonezawa, Yu Yamamori, Hiroko Inoura, Masanori Osawa, Kazuyoshi Ikeda, Kentaro Tomii
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Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-27 Andreia Fortuna, Paulo J. Costa
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Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-24 Dakota L. Folmsbee, David R. Koes, Geoffrey R. Hutchison
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Hot-Spot Residue-Based Virtual Screening of Novel Selective Estrogen-Receptor Degraders for Breast Cancer Treatment J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-23 Rupeng Dai, Xueting Bao, Ying Zhang, Yan Huang, Haohao Zhu, Kundi Yang, Bo Wang, Hongmei Wen, Wei Li, Jian Liu
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Metal–Organic Framework Membrane Constructor: A Tool for High-Throughput Construction of Metal–Organic Framework Membrane Models J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-24 Shitong Zhang, Yanjing He, Shengtang Liu, Zhengqing Zhang, Chongli Zhong
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Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein – Confirmed and Potential Ligands J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-22 Luís Queirós-Reis, João R. Mesquita, Andrea Brancale, Marcella Bassetto
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VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-22 Hiroaki Iwata, Taichi Nakai, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yasushi Okuno
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GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-22 Minghua Zhao, Steven X. Xu, Yaning Yang, Min Yuan
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QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-21 Jackson W. Burns, David M. Rogers
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Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα–DNA Complex J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-21 Nuno M. S. Almeida, Semiha Kevser Bali, Deepak James, Cong Wang, Angela K. Wilson
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Ensemble Geometric Deep Learning of Aqueous Solubility J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-21 Mohammad M. Ghahremanpour, Anastasia Saar, Julian Tirado-Rives, William L. Jorgensen
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Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-21 Sudarshan Behera, Sundaram Balasubramanian
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Unified Model to Predict gRNA Efficiency across Diverse Cell Lines and CRISPR-Cas9 Systems J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Zhicheng Zhong, Zeying Li, Jie Yang, Qian Wang
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From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Rohan Gorantla, Alžbeta Kubincová, Andrea Y. Weiße, Antonia S. J. S. Mey
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Introducing the Automated Ligand Searcher J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Luise Jacobsen, Jonathan Hungerland, Vladimir Bačić, Luca Gerhards, Fabian Schuhmann, Ilia A. Solov’yov
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Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte–Water Solutions J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Jiwon Seo, Ravi Singh, Jonghyuk Ryu, Jun-Ho Choi
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Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou, Haiping Hao, Huiyong Sun
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Identification of High-Reliability Regions of Machine Learning Predictions Based on Materials Chemistry J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Evan M. Askenazi, Emanuel A. Lazar, Ilya Grinberg
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ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-21 Shu-Sen Chen, Zack Meyer, Brendan Jensen, Alex Kraus, Allison Lambert, Daniel H. Ess
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Opinion Mining by Convolutional Neural Networks for Maximizing Discoverability of Nanomaterials J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Tong Xie, Yuwei Wan, Haoran Wang, Ina Østrøm, Shaozhou Wang, Mingrui He, Rong Deng, Xinyuan Wu, Clara Grazian, Chunyu Kit, Bram Hoex
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Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-20 Bodhi P. Vani, Akashnathan Aranganathan, Pratyush Tiwary
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Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS) J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-19 Melissa Marciesky, Diana S. Aga, Ian M. Bradley, Nirupam Aich, Carla Ng
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PDBminer to Find and Annotate Protein Structures for Computational Analysis J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-17 Kristine Degn, Ludovica Beltrame, Matteo Tiberti, Elena Papaleo
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Comparative Assessment of Pose Prediction Accuracy in RNA–Ligand Docking J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-16 Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith
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Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-16 Lihua Dong, Yongjun Liu
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Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-15 Riccardo Rozza, Pavel Janoš, Alessandra Magistrato
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Ensemble-Based Approaches Ensure Reliability and Reproducibility J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-15 Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Peter V. Coveney
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MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-13 Gianmattia Sgueglia, Michail D. Vrettas, Marco Chino, Alfonso De Simone, Angela Lombardi
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Transmembrane β-Barrel Models of α-Synuclein Oligomers J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-14 Manuela Maurer, Themis Lazaridis
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Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-14 Mingyuan Xu, Hongming Chen
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Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-13 Juan J. Galano-Frutos, Francho Nerín-Fonz, Javier Sancho
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Novel Models for Accurate Estimation of Air–Blood Partitioning: Applications to Individual Compounds and Complex Mixtures of Neutral Organic Compounds J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-13 Ahmad Aakash, Ramsha Kulsoom, Saba Khan, Musab Saeed Siddiqui, Deedar Nabi
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Attention Mechanism-Based Graph Neural Network Model for Effective Activity Prediction of SARS-CoV-2 Main Protease Inhibitors: Application to Drug Repurposing as Potential COVID-19 Therapy J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-13 Yanling Wu, Kun Li, Menglong Li, Xuemei Pu, Yanzhi Guo
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ChatGPT in Drug Discovery: A Case Study on Anticocaine Addiction Drug Development with Chatbots J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-13 Rui Wang, Hongsong Feng, Guo-Wei Wei
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Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-10 Vidushi Sharma, Maxwell Giammona, Dmitry Zubarev, Andy Tek, Khanh Nugyuen, Linda Sundberg, Daniele Congiu, Young-Hye La
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Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases J. Chem. Inf. Model. (IF 5.6) Pub Date : 2023-11-10 Candide Champion, René Gall, Benjamin Ries, Salomé R. Rieder, Emilia P. Barros, Sereina Riniker
更新日期：2023-12-08
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