
样式: 排序: IF: - GO 导出 标记为已读
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GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-24 Sangwoo Park, Chaok Seok
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Predicting In Vivo Compound Brain Penetration Using Multi-task Graph Neural Networks J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-23 Seid Hamzic, Richard Lewis, Sandrine Desrayaud, Cihan Soylu, Mike Fortunato, Grégori Gerebtzoff, Raquel Rodríguez-Pérez
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MA’AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-22 Reagan J. Meredith, Luke Sernau, Anthony S. Serianni
A hybrid experimental–computational method to determine conformational equilibria of molecules in solution has been developed based on the use of redundant nuclear magnetic resonance (NMR) spin–spin coupling constants (spin-couplings; J-couplings), density functional theory (DFT) calculations, and circular statistics. The mathematics that underpins the method, known as MA’AT analysis, is presented
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AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-21 Michael Schauperl, Rajiah Aldrin Denny
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Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-17 Raitis Bobrovs, Emils Edgars Basens, Laura Drunka, Iveta Kanepe, Sofija Matisone, Karlis Kristofers Velins, Victor Andrianov, Gundars Leitis, Diana Zelencova-Gopejenko, Dace Rasina, Aigars Jirgensons, Kristaps Jaudzems
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Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-17 Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu
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Exploring Potential Energy Surfaces Using Reinforcement Machine Learning J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-16 Alexis W. Mills, Joshua J. Goings, David Beck, Chao Yang, Xiaosong Li
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Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid–Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-16 Zenghui Lao, Xuewei Dong, Xianshi Liu, Fangying Li, Yujie Chen, Yiming Tang, Guanghong Wei
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DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-16 Lingyan Wang, Kun Xi, Lizhe Zhu, Lin-Tai Da
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Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-15 Erik Otović, Marko Njirjak, Daniela Kalafatovic, Goran Mauša
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Predicting Protein–Ligand Docking Structure with Graph Neural Network J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-14 Huaipan Jiang, Jian Wang, Weilin Cong, Yihe Huang, Morteza Ramezani, Anup Sarma, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir
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Virtual Screening Expands the Non-Natural Amino Acid Palette for Peptide Optimization J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-14 Kosala N. Amarasinghe, Leonardo De Maria, Christian Tyrchan, Leif A. Eriksson, Jens Sadowski, Dušan Petrović
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Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-13 Manuel A. Llanos, Nicolás Enrique, María L. Sbaraglini, Federico M. Garofalo, Alan Talevi, Luciana Gavernet, Pedro Martín
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Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-13 Pedro R. Magalhães, Pedro B. P. S. Reis, Diogo Vila-Viçosa, Miguel Machuqueiro, Bruno L. Victor
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CROMATIC: Cross-Relationship Map of Cavities from Coronaviruses J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-13 Lydia Siragusa, Gabriele Menna, Fabrizio Buratta, Massimo Baroni, Jenny Desantis, Gabriele Cruciani, Laura Goracci
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Translocation Mechanism of Allosteric Sodium Ions in β2-Adrenoceptor J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-13 Xueying Wang, Shuguang Yuan, H. C. Stephen Chan
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MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-13 Hao Wang, Xiaolin Pan, Yueqing Zhang, Xingyu Wang, Xudong Xiao, Changge Ji
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Chemical Information and Computational Modeling of Targeting Hybrid Nucleic Acid Structures of PIM1 Sequences by Synthetic Pyrrole-Imidazole Carboxamide Drugs J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-10 Soma Roy, Santanu Bhattacharya
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Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-10 Adan Gallardo, Brandon M. Bogart, Bercem Dutagaci
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iRaPCA and SOMoC: Development and Validation of Web Applications for New Approaches for the Clustering of Small Molecules J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-10 Denis N. Prada Gori, Manuel A. Llanos, Carolina L. Bellera, Alan Talevi, Lucas N. Alberca
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Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-09 Yongjun Zang, Luyang Tai, Yuanyang Hu, Yu Wang, Hongbin Sun, Xiaoan Wen, Haoliang Yuan, Liang Dai
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Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-09 Maria Antonietta La Serra, Pietro Vidossich, Isabella Acquistapace, Anand K. Ganesan, Marco De Vivo
Here, we show that alchemical free energy calculations can quantitatively compute the effect of mutations at the protein–protein interface. As a test case, we have used the protein complex formed by the small Rho-GTPase CDC42 and its downstream effector PAK1, a serine/threonine kinase. Notably, the CDC42/PAK1 complex offers a wealth of structural, mutagenesis, and binding affinity data because of its
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Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-09 Vincenzo Laveglia, Andrea Giachetti, Davide Sala, Claudia Andreini, Antonio Rosato
Thirty-eight percent of protein structures in the Protein Data Bank contain at least one metal ion. However, not all these metal sites are biologically relevant. Cations present as impurities during sample preparation or in the crystallization buffer can cause the formation of protein–metal complexes that do not exist in vivo. We implemented a deep learning approach to build a classifier able to distinguish
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Shry: Application of Canonical Augmentation to the Atomic Substitution Problem J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-09 Genki Imam Prayogo, Andrea Tirelli, Keishu Utimula, Kenta Hongo, Ryo Maezono, Kousuke Nakano
A common approach for studying a solid solution or disordered system within a periodic ab initio framework is to create a supercell in which certain amounts of target elements are substituted with other elements. The key to generating supercells is determining how to eliminate symmetry-equivalent structures from many substitution patterns. Although the total number of substitutions is on the order
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Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-08 Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dongsheng Cao, Zhe Wang, Tingjun Hou
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How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-08 Jeremy Morere, Cécilia Hognon, Tom Miclot, Tao Jiang, Elise Dumont, Giampaolo Barone, Antonio Monari, Emmanuelle Bignon
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Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-08 Salomé R. Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emilia P. Barros, Philippe H. Hünenberger, Sereina Riniker
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett’s acceptance ratio. Replica-exchange enveloping distribution sampling (RE-EDS), on the other hand, allows for the sampling of multiple end-states in a single simulation
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Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-07 Daniel Bustos, Erix W. Hernández-Rodríguez, Horacio Poblete, Jans Alzate-Morales, Cecilia Challier, Cristhian Boetsch, Ariela Vergara-Jaque, Paola Beassoni
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On the Possibility That Bond Strain Is the Mechanism of RING E3 Activation in the E2-Catalyzed Ubiquitination Reaction J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-07 Jay-Anne K. Johnson, Isaiah Sumner
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Exploring the Chemical Space of Urease Inhibitors to Extract Meaningful Trends and Drivers of Activity J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-06 Natália Aniceto, Vasco D. B. Bonifácio, Rita C. Guedes, Nuno Martinho
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Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-06 Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, Serge Perez, Vincent Leroux, Isaure Chauvot de Beauchêne, Dominique Mias-Lucquin, Marie-Dominique Devignes, Ivan Rivalta, Bernard Maigret
Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild type and five variants that emerged in late 2020, focusing on the structure and dynamics of the spike protein interface with the human angiotensin-converting
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Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-06 Minjie Kang, Zhicheng Zuo, Zhixiang Yin, Jianrong Gu
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MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-06 Myeonghun Lee, Kyoungmin Min
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CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-01 Sree Kavya Penneru, Moumita Saharay, Marimuthu Krishnan
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Retro Drug Design: From Target Properties to Molecular Structures J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-02 Yuhong Wang, Sam Michael, Shyh-Ming Yang, Ruili Huang, Kennie Cruz-Gutierrez, Yaqing Zhang, Jinghua Zhao, Menghang Xia, Paul Shinn, Hongmao Sun
To deliver more therapeutics to more patients more quickly and economically is the ultimate goal of pharmaceutical researchers. The advent and rapid development of artificial intelligence (AI), in combination with other powerful computational methods in drug discovery, makes this goal more practical than ever before. Here, we describe a new strategy, retro drug design, or RDD, to create novel small-molecule
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Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-06-02 Louis Bellmann, Raphael Klein, Matthias Rarey
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Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-31 Hiraku Oshima, Yuji Sugita
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Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-31 Yuyang Wang, Rishikesh Magar, Chen Liang, Amir Barati Farimani
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PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-27 Xu Yan, Yingfeng Lu, Zhen Li, Qing Wei, Xin Gao, Sheng Wang, Song Wu, Shuguang Cui
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Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-25 Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane, Rajendra Joshi
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Exploring the Spike-hACE 2 Residue–Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63 J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-26 José X. Lima Neto, Davi S. Vieira, Jones de Andrade, Umberto Laino Fulco
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Differential Multimolecule Fingerprint for Similarity Search─Making Use of Active and Inactive Compound Sets in Virtual Screening J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-25 Michael C. Hutter
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BenzAI: A Program to Design Benzenoids with Defined Properties Using Constraint Programming J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-25 Adrien Varet, Nicolas Prcovic, Cyril Terrioux, Denis Hagebaum-Reignier, Yannick Carissan
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Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-24 Sinan Kardas, Mathieu Fossépré, Vincent Lemaur, Antony E. Fernandes, Karine Glinel, Alain M. Jonas, Mathieu Surin
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IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-24 Chaofeng Lou, Hongbin Yang, Jiye Wang, Mengting Huang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang
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Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-24 Abdul Basit, Ajeet Kumar Yadav, Pradipta Bandyopadhyay
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Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-20 Xiyu Chen, Sigrid Leyendecker, Henry van den Bedem
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Bias Amplification in Gender, Gender Identity, and Geographical Affiliation J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-19 Michele Cascella, Thereza A. Soares
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Early Career Perspectives from Large Pharma, Software, and Start-up Companies J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-19 Fiorella Ruggiu, Caitlin Bannan, Andrea Bootsma
We are often approached by PhD students and postdocs who wonder: What are the differences between jobs for computational chemists across different industries? This Perspective aims to answer this question by comparing our personal experiences as early career scientists at a large pharmaceutical company (large pharma), a software vendor (software), and a biotech start-up (start-up) in the format of
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Reconstructing Chromatic-Dispersion Relations and Predicting Refractive Indices Using Text Mining and Machine Learning J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-19 Jiuyang Zhao, Jacqueline M. Cole
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Mechanistic Insights into the Anaerobic Degradation of Globally Abundant Dihydroxypropanesulfonate Catalyzed by the DHPS-Sulfolyase (HpsG) J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-18 Lijuan Yan, Yongjun Liu
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Computational Analysis of the SARS-CoV-2 RBD–ACE2-Binding Process Based on MD and the 3D-RISM Theory J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-18 Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano
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Transferable Classical Force Field for Pure and Mixed Metal Halide Perovskites Parameterized from First-Principles J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-16 Juan Antonio Seijas-Bellido, Bipasa Samanta, Karen Valadez-Villalobos, Juan Jesús Gallardo, Javier Navas, Salvador R. G. Balestra, Rafael María Madero Castro, José Manuel Vicent-Luna, Shuxia Tao, Maytal Caspary Toroker, Juan Antonio Anta
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ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-16 Yuxiang Wang, Alper Kiziltas, Patrick Blanchard, Tiffany R. Walsh
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An In Silico Explainable Multiparameter Optimization Approach for De Novo Drug Design against Proteins from the Central Nervous System J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-17 Navneet Bung, Sowmya Ramaswamy Krishnan, Arijit Roy
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Mechanistic Modeling of Monoglyceride Lipase Covalent Modification Elucidates the Role of Leaving Group Expulsion and Discriminates Inhibitors with High and Low Potency J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-17 Francesca Galvani, Laura Scalvini, Silvia Rivara, Alessio Lodola, Marco Mor
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Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-17 Chao Yang, Yingkai Zhang
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Deep-Learning-Based End-to-End Predictions of CO2 Capture in Metal–Organic Frameworks J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-16 Cunxing Lu, Xili Wan, Xuhao Ma, Xinjie Guan, Aichun Zhu
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Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide–Peptide and Peptide–Solvent Interactions J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-13 Xiang Cai, Wei Han
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GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems J. Chem. Inf. Model. (IF 4.956) Pub Date : 2022-05-13 Timothy Cholko, Shivansh Kaushik, Kingsley Y. Wu, Ruben Montes, Chia-en A. Chang