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ORCIDJournal of Chemical Information and Modeling, Volume 64
Volume 64, Number 1, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr.
:
In Memoriam: Dr. George W. A. Milne. 1-2 - Andrew Rusinko III, Mohammad A. Rezaei, Lukas Friedrich, Hans-Peter Buchstaller, Daniel Kuhn, Ashwini Ghogare:
AIDDISON: Empowering Drug Discovery with AI/ML and CADD Tools in a Secure, Web-Based SaaS Platform. 3-8 - Esther Heid, Kevin P. Greenman, Yunsie Chung, Shih-Cheng Li, David E. Graff, Florence H. Vermeire, Haoyang Wu, William H. Green Jr., Charles McGill:
Chemprop: A Machine Learning Package for Chemical Property Prediction. 9-17 - Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov:
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals. 18-25 - Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, Marc Baaden, Patrick Fuchs, Tatiana Galochkina, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora, Antoine Taly:
A Perspective on the Prospective Use of AI in Protein Structure Prediction. 26-41 - Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko:
When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. 42-56 - Zhuohang Yu, Zengrui Wu, Ze Wang, Yimeng Wang, Moran Zhou, Weihua Li, Guixia Liu, Yun Tang:
Network-Based Methods and Their Applications in Drug Discovery. 57-75 - Chunxiang Peng, Fang Liang, Yuhao Xia, Kai-Long Zhao, Minghua Hou, Gui-Jun Zhang:
Recent Advances and Challenges in Protein Structure Prediction. 76-95 - Ning-Ning Wang, Bei Zhu, Xin-Liang Li, Shao Liu, Jian-Yu Shi, Dong-Sheng Cao:
Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities. 96-109 - Ruihan Zhang, Xingran Xie, Dongxuan Ni, Hairong Wang, Jin Li, Weilie Xiao:
MT-EpiPred: Multitask Learning for Prediction of Small-Molecule Epigenetic Modulators. 110-118 - Yuto Matsumoto, Hiroaki Gotoh:
Compound Classification and Consideration of Correlation with Chemical Descriptors from Articles on Antioxidant Capacity Using Natural Language Processing. 119-127 - Arnab Bose, Gabriel A. Valdivia-Berroeta, Nina C. Gonnella:
Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods. 128-137 - Jiwon Seo, Ravi Singh, Jonghyuk Ryu, Jun-Ho Choi:
Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions. 138-149 - Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H. Sauer, Magnus Wolf-Watz:
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. 150-163 - Alejandro Rivera-Pousa, Raúl Lois-Cuns, Martín Otero-Lema, Hadrián Montes-Campos, Trinidad Méndez-Morales, Luis M. Varela:
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids. 164-177 - Gaurav Jhaa, Pattath D. Pancharatna, Musiri M. Balakrishnarajan:
Alternatives for Epoxides in Graphene Oxide. 178-188 - Aitor Valdivia, F. Javier Luque, Salomé Llabrés:
Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations. 189-204 - Jacqueline C. Calderón, Eva Plut, Max Keller, Chiara Cabrele, Oliver Reiser, Francesco L. Gervasio, Timothy Clark:
Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. 205-218 - Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey:
Redocking the PDB. 219-237 - Zhong-Hao Ren, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Zheng-Wei Li, Shanwen Zhang, Xiangxiang Zeng, Yi-Fan Shang:
SiSGC: A Drug Repositioning Prediction Model Based on Heterogeneous Simplifying Graph Convolution. 238-249 - Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio:
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. 250-264 - Toby E. King, James R. Humphrey, Charles A. Laughton, Neil R. Thomas, Jonathan D. Hirst:
Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. 265-275 - Afshin Zamani Zakaria, Alpeshkumar K. Malde, Tim Gould:
Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers. 276-288 - Bing Rao, Xuan Yu, Jie Bai, Jun Hu:
E2EATP: Fast and High-Accuracy Protein-ATP Binding Residue Prediction via Protein Language Model Embedding. 289-300 - Jiaxuan Li, Lei Wang, Zefeng Zhu, Chen Song:
Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. 301-315 - Haoqing Yu, Ruheng Wang, Jianbo Qiao, Leyi Wei:
Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. 316-326
Volume 64, Number 2, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Jawad Chowdhury, Charles Fricke, Olajide Bamidele, Mubarak Bello, Wenqiang Yang, Andreas Heyden, Gabriel Terejanu:
Invariant Molecular Representations for Heterogeneous Catalysis. 327-339 - Gen Li, Sijie Yao, Long Fan:
ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks. 340-347 - Ya Chen, Thomas Seidel, Roxane Axel Jacob, Steffen Hirte, Angelica Mazzolari, Alessandro Pedretti, Giulio Vistoli, Thierry Langer, Filip Miljkovic, Johannes Kirchmair:
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. 348-358 - Yu Yin, Zhen Yang, Na Li, Xuan Yu, Mei-ling Chen, Meng Wang, Xiao-liang Ren:
Least Absolute Shrinkage and Selection Operator-Based Prediction of the Binding Constant of p-Sulfonatocalix[6]/[8]arenes with Alkaloids. 359-377 - Julian M. Delgado, Péter R. Nagy, Sameer Varma:
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes. 378-392 - Mateus Sá Magalhães Serafim, Thales Kronenberger, Rafael Eduardo Oliveira Rocha, Amanda Del Rio Abreu Rosa, Thaysa Lara Gonçalves Mello, Antti Poso, Rafaela Salgado Ferreira, Jonatas Santos Abrahão, Erna Geessien Kroon, Bruno Eduardo Fernandes Mota, Vinicius Gonçalves Maltarollo:
Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. 393-411 - Marco Foscato, Giovanni Occhipinti, Sondre H. Eliasson, Vidar R. Jensen:
Automated de Novo Design of Olefin Metathesis Catalysts: Computational and Experimental Analysis of a Simple Thermodynamic Design Criterion. 412-424 - Matthew S. Smith, Ian S. Knight, Rian C. Kormos, Joseph G. Pepe, Peter Kunach, Marc I. Diamond, Sarah H. Shahmoradian, John J. Irwin, William F. Degrado, Brian K. Shoichet:
Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. 425-434 - William T. Higgins, Sandip Vibhute, Chad Bennett, Steffen Lindert:
Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. 435-448 - Midhun K. Madhu, Kunal Shewani, Rajesh K. Murarka:
Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. 449-469 - Amanda C. Macke, Jacob E. Stump, Maria S. Kelly, Jamie Rowley, Vageesha Herath, Sarah Mullen, Ruxandra I. Dima:
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. 470-482 - Deepak Ahire, Charles Mariasoosai, Siavosh Naji-Talakar, Senthil Natesan, Bhagwat Prasad:
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches. 483-498 - Maya Petgrave, Shubham Devesh Ramgoolam, Aravindhan Ganesan:
Deciphering the Molecular Association of Human CRIP1a with an Agonist-Bound Cannabinoid Receptor 1. 499-517 - Charlotte Bouquiaux, Benoît Champagne, Pierre Beaujean:
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes. 518-531 - Yusuke Miyazaki, Wataru Shinoda:
pSPICA Force Field Extended for Proteins and Peptides. 532-542 - Santiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla:
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. 543-554 - Juan I. Felice, Verónica Milesi, Gabriel Fabricius:
Exploration of the Parameter Space of an Ion Channel Kinetic Model by a Markov-Chain-Based Methodology. 555-562
Volume 64, Number 3, February 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Jinlu Zhang, Yin Fang, Xin Shao, Huajun Chen, Ningyu Zhang, Xiaohui Fan:
The Future of Molecular Studies through the Lens of Large Language Models. 563-566 - Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess:
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. 567-574 - Tao Shen, Jiale Guo, Zunsheng Han, Gao Zhang, Qingxin Liu, Xinxin Si, Dongmei Wang, Song Wu, Jie Xia:
AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. 575-583 - Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr, Gianni De Fabritiis:
PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data. 584-589 - Robert I. Horne, Jared Wilson-Godber, Alicia González Díaz, Z. Faidon Brotzakis, Srijit Seal, Rebecca C. Gregory, Andrea Possenti, Sean Chia, Michele Vendruscolo:
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. 590-596 - Andre Nicolle, Sili Deng, Matthias Ihme, Nursulu Kuzhagaliyeva, Emad Al Ibrahim, Aamir Farooq:
Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. 597-620 - Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F. Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L. Brooks III, Nathalie Reuter:
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. 621-626 - Hongshuo Huang, Rishikesh Magar, Amir Barati Farimani:
Pretraining Strategies for Structure Agnostic Material Property Prediction. 627-637 - Surya Prakash Tiwari, Wei Shi, Samir Budhathoki, James Baker, Ali K. Sekizkardes, Lingxiang Zhu, Victor A. Kusuma, David P. Hopkinson, Janice A. Steckel:
Creation of Polymer Datasets with Targeted Backbones for Screening of High-Performance Membranes for Gas Separation. 638-652 - Gregory W. Kyro, Anton Morgunov, Rafael I. Brent, Victor S. Batista:
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. 653-665 - Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen:
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. 666-676 - Hyeonsu Kim, Kyunghoon Lee, Jun Hyeong Kim, Woo Youn Kim:
Deep Learning-Based Chemical Similarity for Accelerated Organic Light-Emitting Diode Materials Discovery. 677-689 - Lewis Y. Geer, Stephen E. Stein, William Gary Mallard, Douglas J. Slotta:
AIRI: Predicting Retention Indices and Their Uncertainties Using Artificial Intelligence. 690-696 - Prudencio Tossou, Cas Wognum, Michael Craig, Hadrien Mary, Emmanuel Noutahi:
Real-World Molecular Out-Of-Distribution: Specification and Investigation. 697-711 - Alec J. Sanchez, Sarah Maier, Krishnan Raghavachari:
Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning. 712-723 - Minfei Ma, Xinben Zhang, Liping Zhou, Zijian Han, Yulong Shi, Jintian Li, Leyun Wu, Zhijian Xu, Weiliang Zhu:
D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. 724-736 - Weichen Bo, Yangqin Duan, Yurong Zou, Ziyan Ma, Tao Yang, Peng Wang, Tao Guo, Zhiyuan Fu, Jianmin Wang, Linchuan Fan, Jie liu, Taijin Wang, Lijuan Chen:
Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors. 737-748 - Susanta Das, Kenneth M. Merz Jr.:
Molecular Gas-Phase Conformational Ensembles. 749-760 - Qing Wang, Xuegang Fu, Yuting Yan, Tao Liu, Yuting Xie, Xiaoqing Song, Yu Zhou, Min Xu, Ping Wang, Peng Fu, Jianhui Huang, Niu Huang:
Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. 761-774 - Justin K. Kirkland, Jugal Kumawat, Maliheh Shaban Tameh, Tyson Tolman, Allison C. Lambert, Graham R. Lief, Qing Yang, Daniel H. Ess:
Machine Learning Models for Predicting Zirconocene Properties and Barriers. 775-784 - Mingqiong Tong, Peng Liu, Chaoqun Li, Zhongyu Zhang, Wan Sun, Pingxuan Dong, Na Fan, Xiaoyue Wang, Jing Liu, Chao Lv, Zanxia Cao, Yan Wang:
Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. 785-798 - Jyotirmoy Deb, Lakshi Saikia, Kripa Dristi Dihingia, G. Narahari Sastry:
ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT. 799-811 - Luke Landry, Pengfei Li:
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. 812-824 - Christian Hölzer, Igor Gordiy, Stefan Grimme, Markus Bursch:
Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set. 825-836 - Shalmali Kharche, Manjul Yadav, Vrushali Hande, Shikha Prakash, Durba Sengupta:
Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. 837-850 - Xu Zhou, Zhiqiang Wei, Hao Lu, Jiaqi He, Yuan Gao, Xiaotong Hu, Cunji Wang, Yujie Dong, Hao Liu:
Large-Scale Molecular Dynamics Simulation Based on Heterogeneous Many-Core Architecture. 851-861 - Nurit Haspel, Hyunbum Jang, Ruth Nussinov:
Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. 862-873 - Nopawit Khamto, Kraikrit Utama, Panida Boontawee, Atchara Janthong, Suriya Tatieng, Supakorn Arthan, Vachira Choommongkol, Padchanee Sangthong, Chavi Yenjai, Nuttee Suree, Puttinan Meepowpan:
Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations. 874-891 - 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:
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. 892-904 - Sayyed Jalil Mahdizadeh, Michael Stier, Antonio Carlesso, Aurore Lamy, Melissa Thomas, Leif A. Eriksson:
Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase. 905-917 - Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei:
Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. 918-932 - Christopher Kang, Alyson Shoji, Christophe Chipot, Rui Sun:
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. 933-943 - Rajwinder Kaur, Stacey D. Wetmore:
Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. 944-959 - Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda:
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. 960-973 - Yunhao Mei, Yong Shen:
Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. 974-982 - Anupom Roy, Mikko Karttunen:
A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase. 983-1003 - Ian S. Knight, Olivier Mailhot, Khanh G. Tang, John J. Irwin:
DockOpt: A Tool for Automatic Optimization of Docking Models. 1004-1016 - Sana Akhter, Zhichao Tang, Jinan Wang, Mercy Haboro, Erik D. Holmstrom, Jingxin Wang, Yinglong Miao:
Mechanism of Ligand Binding to Theophylline RNA Aptamer. 1017-1029 - Zora Novakova, Zahra Aliakbar Tehrani, Radek Jurok, Lucia Motlova, Zsófia Kutil, Jiri Pavlicek, Shivam Shukla, Cindy J. Choy, Barbora Havlinova, Petra Baranova, Clifford E. Berkman, Martin Kuchar, Jirí Cerný, Cyril Barinka:
Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. 1030-1042 - Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu:
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. 1043-1049 - Jiashuo Zhang, Ruheng Wang, Leyi Wei:
MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. 1050-1065 - Shuang Guo, Yuwei Liu, Yue Sun, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhi, Yakun Zhang, Jing Gan, Shangwei Ning:
Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer. 1066-1080 - Emma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot:
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. 1081-1091 - Guolun Zhong, Lei Deng:
ACPScanner: Prediction of Anticancer Peptides by Integrated Machine Learning Methodologies. 1092-1104 - Farzad Molani, Simon Webb, Art E. Cho:
Correction to "Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy". 1105 - Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn, Lonny R. Levin, Jochen Buck, Robert W. Myers, Stacia Kargman, Nigel Liverton, Peter T. Meinke, David J. Huggins:
Addition to "Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation". 1106
Volume 64, Number 4, February 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Ronaldo C. Prati, Bruno S. M. Rodrigues, Iberis Aragão, Thereza A. Soares, Marcos G. Quiles, Juarez L. F. Da Silva:
The Impact of Interdisciplinary, Gender and Geographic Distributions on the Citation Patterns of the Journal of Chemical Information and Modeling. 1107-1111 - Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu:
Molecular Contrastive Pretraining with Collaborative Featurizations. 1112-1122 - Benson Chen, Mohammad M. Sultan, Theofanis Karaletsos:
Compositional Deep Probabilistic Models of DNA-Encoded Libraries. 1123-1133 - Seongwon Kim, Parisa Mollaei, Akshay Antony, Rishikesh Magar, Amir Barati Farimani:
GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models. 1134-1144 - Benjamin Kaufman, Edward C. Williams, Carl Underkoffler, Ryan Pederson, Narbe Mardirossian, Ian Watson, John Parkhill:
COATI: Multimodal Contrastive Pretraining for Representing and Traversing Chemical Space. 1145-1157 - Kathryn Klarich, Brian Goldman, Trevor Kramer, Patrick Riley, W. Patrick Walters:
Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases. 1158-1171 - Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. 1172-1186 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Band Gaps of Inorganic Materials Using a Gradient Boosted and Statistical Feature Selection Workflow. 1187-1200 - Frédéric Célerse, Matthew D. Wodrich, Sergi Vela, Simone Gallarati, Raimon Fabregat, Veronika Jurásková, Clémence Corminboeuf:
From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials. 1201-1212 - Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou:
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. 1213-1228 - Juan F. Avellaneda-Tamayo, Ana L. Chávez-Hernández, Diana L. Prado-Romero, José L. Medina-Franco:
Chemical Multiverse and Diversity of Food Chemicals. 1229-1244 - Peter Ertl:
Database of 4 Million Medicinal Chemistry-Relevant Ring Systems. 1245-1250 - Chen Cheng, Paul Beroza:
Shape-Aware Synthon Search (SASS) for Virtual Screening of Synthon-Based Chemical Spaces. 1251-1260 - Yang Wang, Yi Zhou, Ke Du:
Enumeration, Nomenclature, and Stability Rules of Carbon Nanobelts. 1261-1276 - Andrew S. Lee, Sarah Elliott, Hassan Harb, Logan T. Ward, Ian T. Foster, Larry A. Curtiss, Rajeev S. Assary:
Emin: A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability. 1277-1289 - Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts:
Parameterization of General Organic Polymers within the Open Force Field Framework. 1290-1305 - José E. González, Rafael Besse, Matheus P. Lima, Juarez L. F. Da Silva:
Decoding Van der Waals Impact on Chirality Transfer in Perovskite Structures: Density Functional Theory Insights. 1306-1318 - Xiaojie Jin, Min Zhang, Beibei Fu, Mi Li, Jingyi Yang, Zhiming Zhang, Chenghao Li, Huijuan Zhang, Haibo Wu, Weiwei Xue, Yongqi Liu:
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. 1319-1330 - Colin L. Welsh, Lalima K. Madan:
Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. 1331-1346 - Akhil Kumar, Manisha Sharma, Harshwardhan H. Katkar:
Peripheral Linker Mediates Acyl Carrier Protein's Recognition of Dehydratase and Stabilizes Type-I Mycobacterium tuberculosis Fatty Acid Synthase. 1347-1360 - Imane Euldji, Widad Benmouloud, Kamil Paduszynski, Cherif Si-Moussa, Othmane Benkortbi:
Hybrid Improved Grey Wolf Support Vector Regression Algorithm for Modeling Solubilities of APIs in Pure Ionic Liquids: σ-Profile Descriptors. 1361-1376 - Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo:
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. 1377-1393 - Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu:
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. 1394-1406 - Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu:
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. 1407-1418
Volume 64, Number 5, March 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Marjolein T. Oostrom, Sean M. Colby, Thomas O. Metz:
DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool. 1419-1424 - Ewelina Jamrozik, Marek Smieja, Sabina Podlewska:
ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation. 1425-1432 - Gao Tu, Tingting Fu, Guoxun Zheng, Binbin Xu, Rongpei Gou, Ding Luo, Panpan Wang, Weiwei Xue:
Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. 1433-1455 - Yunjiang Zhang, Shuyuan Li, Kong Meng, Shaorui Sun:
Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction. 1456-1472 - Juliette Martin:
AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility. 1473-1480 - Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis:
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. 1481-1485 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks. 1486-1501 - Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng:
MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. 1502-1511 - Fernando Garcia-Escobar, Toshiaki Taniike, Keisuke Takahashi:
MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models. 1512-1521 - Sung Wook Moon, Seung Kyu Min:
Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm. 1522-1532 - Pattipong Wisanpitayakorn, Sitanan Sartyoungkul, Alongkorn Kurilung, Yongyut Sirivatanauksorn, Wonnop Visessanguan, Nuankanya Sathirapongsasuti, Sakda Khoomrung:
Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data. 1533-1542 - Xiaohe Xu, Weijie Han, Xiangzhen Ning, Chengdong Zang, Chengcheng Xu, Chen Zeng, Chengtao Pu, Yanmin Zhang, Yadong Chen, Haichun Liu:
Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. 1543-1559 - Gregory A. Landrum, Sereina Riniker:
Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. 1560-1567 - Hatem Helal, Jesun Firoz, Jenna A. Bilbrey, Henry Sprueill, Kristina M. Herman, Mario Michael Krell, Tom Murray, Manuel Lopez Roldan, Mike Kraus, Ang Li, Payel Das, Sotiris S. Xantheas, Sutanay Choudhury:
Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units. 1568-1580 - Camila M. Clemente, Juan M. Prieto, Marcelo A. Marti:
Unlocking Precision Docking for Metalloproteins. 1581-1592 - Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino:
Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. 1593-1604 - Jochem Nelen, Miguel Carmena-Bargueño, Carlos Martinez-Cortes, Alejandro Rodríguez-Martínez, José Manuel Villalgordo-Soto, Horacio Pérez Sánchez:
ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery. 1605-1614 - Tien-Sheng Tseng, Chao-Chang Lee, Po-Juei Chen, Chiu-Yuen Lin, Wang-Chuan Chen, Yu-Ching Lee, Jiun-Han Lin, Kaun-Wen Chen, Keng-Chang Tsai:
Structure-Guided Discovery of PD-1/PD-L1 Interaction Inhibitors: Peptide Design, Screening, and Optimization via Computation-Aided Phage Display Engineering. 1615-1627 - Dávid Zajacek, Adriána Dunárová, Lukás Bucinský, Marek Steklác:
Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate. 1628-1643 - Hong Ha Nguyen, Jim Tufts, David D. L. Minh:
On Inactivation of the Coronavirus Main Protease. 1644-1656 - Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker:
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. 1657-1681 - 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:
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains. 1682-1690 - Sebastian Anila, Sergey A. Samsonov:
Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. 1691-1703 - Kaylen R. Meeks, Juan Ji, Mykola V. Protopopov, Olga O. Tarkhanova, Yurii S. Moroz, John J. Tanner:
Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography. 1704-1718 - Kun Wang, Ben Cao, Tao Ma, Yunzhu Zhao, Yanfen Zheng, Bin Wang, Shihua Zhou, Qiang Zhang:
Storing Images in DNA via base128 Encoding. 1719-1729 - Romanos Fasoulis, Maurício Menegatti Rigo, Gregory Lizée, Dinler A. Antunes, Lydia E. Kavraki:
APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. 1730-1750 - Zuojun Yang, Yuhan Wu, Hao Liu, Li He, Xiaoyuan Deng:
AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides. 1751-1762 - Nutaya Pravalphruekul, Maytus Piriyajitakonkij, Phond Phunchongharn, Supanida Piyayotai:
Correction to "De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder". 1763
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