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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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Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Xudong Yang, Chengwen Liu, Pengyu Ren
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Electronic Couplings for Triplet–Triplet Annihilation Upconversion in Crystal Rubrene J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Aitor Diaz-Andres, Claire Tonnelé, David Casanova
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LigandDiff: de Novo Ligand Design for 3D Transition Metal Complexes with Diffusion Models J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Hongni Jin, Kenneth M. Merz, Jr.
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TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Raul P. Pelaez, Guillem Simeon, Raimondas Galvelis, Antonio Mirarchi, Peter Eastman, Stefan Doerr, Philipp Thölke, Thomas E. Markland, Gianni De Fabritiis
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Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-14 Candide Champion, Philippe H. Hünenberger, Sereina Riniker
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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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Deep learning with plasma plume image sequences for anomaly detection and prediction of growth kinetics during pulsed laser deposition npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-14 Sumner B. Harris, Christopher M. Rouleau, Kai Xiao, Rama K. Vasudevan
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Evolution-guided Bayesian optimization for constrained multi-objective optimization in self-driving labs npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-13 Andre K. Y. Low, Flore Mekki-Berrada, Abhishek Gupta, Aleksandr Ostudin, Jiaxun Xie, Eleonore Vissol-Gaudin, Yee-Fun Lim, Qianxiao Li, Yew Soon Ong, Saif A. Khan, Kedar Hippalgaonkar
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InChI isotopologue and isotopomer specifications J. Cheminfom. (IF 8.6) Pub Date : 2024-05-14 Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma L. Schymanski
This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolved chemical entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue
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One chiral fingerprint to find them all J. Cheminfom. (IF 8.6) Pub Date : 2024-05-13 Markus Orsi, Jean-Louis Reymond
Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral. Herein we report MAP4C, a chiral version of our previously reported fingerprint MAP4, which lists MinHashes computed from character strings containing the SMILES of all pairs of circular substructures up to a diameter
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Restriction on molecular fluxionality by substitution: A case study for the 1,10‐dicyanobullvalene J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-14 Bin‐Bin Pei, Hongjuan Yang, Cai‐Yue Gao, Yuan Man, Yonggang Yang, Si‐Dian Li
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Computational assessment of the use of graphene‐based nanosheets as PtII chemotherapeutics delivery systems J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-14 Daniele Belletto, Vincenzo Vigna, Pierraffaele Barretta, Fortuna Ponte, Gloria Mazzone, Stefano Scoditti, Emilia Sicilia
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t2g$$ {t}_{2g} $$d$$ d $$ orbital ordering patterns in KBF3$$ {}_3 $$ (B = Sc, Ti, Fe, Co) perovskites J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-14 Fabien Pascale, Philippe D'Arco, Sami Mustapha, Roberto Dovesi
The orbital ordering (OO) resulting from the partial occupancy of the subshell of the transition metals in KBF (B = Sc, Ti, Ffe, Co) perovskites, and the many possible patterns arising from the coupling between the B sites, have been investigated at the quantum mechanical level ( Gaussian type basis set, B3LYP hybrid functional) in a 40 atoms supercell. The numerous patterns are distributed into 162
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Modulating Efficiency and Color of Thermally Activated Delayed Fluorescence by Rationalizing the Substitution Effect J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-13 Alejandro Jodra, Marco Marazzi, Luis Manuel Frutos, Cristina García-Iriepa
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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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Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-13 Aurélien Moncomble, Jean‐Paul Cornard
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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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Distance plus attention for binding affinity prediction J. Cheminfom. (IF 8.6) Pub Date : 2024-05-12 Julia Rahman, M. A. Hakim Newton, Mohammed Eunus Ali, Abdul Sattar
Protein-ligand binding affinity plays a pivotal role in drug development, particularly in identifying potential ligands for target disease-related proteins. Accurate affinity predictions can significantly reduce both the time and cost involved in drug development. However, highly precise affinity prediction remains a research challenge. A key to improve affinity prediction is to capture interactions
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Strain engineering the spin-valley coupling of the R-stacking sliding ferroelectric bilayer 2H-VX2 (X = S, Se, Te) npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-10 Jiayu Ma, Xin Luo, Yue Zheng
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Growing strings in a chemical reaction space for searching retrosynthesis pathways npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-10 Federico Zipoli, Carlo Baldassari, Matteo Manica, Jannis Born, Teodoro Laino
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CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space J. Cheminfom. (IF 8.6) Pub Date : 2024-05-10 Christina Humer, Rachel Nicholls, Henry Heberle, Moritz Heckmann, Michael Pühringer, Thomas Wolf, Maximilian Lübbesmeyer, Julian Heinrich, Julius Hillenbrand, Giulio Volpin, Marc Streit
Chemical reaction optimization (RO) is an iterative process that results in large, high-dimensional datasets. Current tools allow for only limited analysis and understanding of parameter spaces, making it hard for scientists to review or follow changes throughout the process. With the recent emergence of using artificial intelligence (AI) models to aid RO, another level of complexity has been added
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Ruthenium complexes bearing nile red chromophore and one of its derivative: Theoretical evaluation of PDT‐related properties J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-11 Pierraffaele Barretta, Stefano Scoditti, Daniele Belletto, Fortuna Ponte, Vincenzo Vigna, Gloria Mazzone, Emilia Sicilia
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PointGAT: A Quantum Chemical Property Prediction Model Integrating Graph Attention and 3D Geometry J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Rong Zhang, Rongqing Yuan, Boxue Tian
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Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Mayank Dodia, Jérémy R. Rouxel, Daeheum Cho, Yu Zhang, Daniel Keefer, Mischa Bonn, Yuki Nagata, Shaul Mukamel
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2-in-1 Phase Space Sampling for Calculating the Absorption Spectrum of the Hydrated Electron J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 László Turi, Bence Baranyi, Ádám Madarász
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Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Ivan Isaac Riveros, Ilyas Yildirim
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GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-10 Janghoon Ock, Parisa Mollaei, Amir Barati Farimani
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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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Attention towards chemistry agnostic and explainable battery lifetime prediction npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-10 Fuzhan Rahmanian, Robert M. Lee, Dominik Linzner, Kathrin Michel, Leon Merker, Balazs B. Berkes, Leah Nuss, Helge Sören Stein
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Impact of protein conformations on binding free energy calculations in the beta‐secretase 1 system J. Comput. Chem. (IF 3.0) Pub Date : 2024-05-10 Hannah M. Baumann, David L. Mobley
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Toward Real Chemical Accuracy on Current Quantum Hardware Through the Transcorrelated Method J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-09 Werner Dobrautz, Igor O. Sokolov, Ke Liao, Pablo López Ríos, Martin Rahm, Ali Alavi, Ivano Tavernelli
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Evaluating Polarizable Biomembrane Simulations against Experiments J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Hanne S. Antila, Sneha Dixit, Batuhan Kav, Jesper J. Madsen, Markus S. Miettinen, O. H. Samuli Ollila
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Decarboxylation Mechanism of iso-Orotate Decarboxylase Revisited J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Jing Xiong, Dingguo Xu
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Fully Quantum Simulation of Polaritonic Vibrational Spectra of Large Cavity-Molecule System J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Qi Yu, Joel M. Bowman
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QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Maximilian C. Pöverlein, Andreas Hulm, Johannes C. B. Dietschreit, Jörg Kussmann, Christian Ochsenfeld, Ville R. I. Kaila
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Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Basak Koca Fındık, Majid Jafari, Lin Frank Song, Zhen Li, Viktorya Aviyente, Kenneth M. Merz, Jr.
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Physical Prior Mean Function-Driven Gaussian Processes Search for Minimum-Energy Reaction Paths with a Climbing-Image Nudged Elastic Band: A General Method for Gas-Phase, Interfacial, and Bulk-Phase Reactions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-08 Chong Teng, Yang Wang, Junwei Lucas Bao
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Quantum Mechanical Versus Polarizable Embedding Schemes: A Study of the Xray Absorption Spectra of Aqueous Ammonia and Ammonium J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Sarai Dery Folkestad, Alexander C. Paul, Regina Paul née Matveeva, Peter Reinholdt, Sonia Coriani, Michael Odelius, Henrik Koch
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Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant
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Sparse-Stochastic Fragmented Exchange for Large-Scale Hybrid Time-Dependent Density Functional Theory Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-05-07 Mykola Sereda, Tucker Allen, Nadine C. Bradbury, Khaled Z. Ibrahim, Daniel Neuhauser
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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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The Bell-Evans-Polanyi relation for hydrogen evolution reaction from first-principles npj Comput. Mater. (IF 9.7) Pub Date : 2024-05-08 Timothy T. Yang, Wissam A. Saidi