Journal of chemical information and modeling

Keyphrases

Publications

volume 64, number 9, 2024

Rohan Chandraghatgi, Hai-Feng Ji, Gail L Rosen, Bahrad A Sokhansanj
Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening. Journal of chemical information and modeling 64 (9) (2024)
Tzu-Hsien Yang
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. Journal of chemical information and modeling 64 (9) (2024)
Paige E Bowling, Saswata Dasgupta, John M Herbert
Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. Journal of chemical information and modeling 64 (9) (2024)
Pieter B Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M Kaiser
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. Journal of chemical information and modeling 64 (9) (2024)
Marzieh Saeedimasine, Roja Rahmani, Alexander P Lyubartsev
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. Journal of chemical information and modeling 64 (9) (2024)
Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R Houston
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening. Journal of chemical information and modeling 64 (9) (2024)
Haopeng Ai, Deyin Wu, Huihao Zhou, Jun Xu, Qiong Gu
dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks. Journal of chemical information and modeling 64 (9) (2024)
Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey V Shvetsov
DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories. Journal of chemical information and modeling 64 (9) (2024)
Bingxin Zhou, Lirong Zheng, Banghao Wu, Yang Tan, Outongyi Lv, Kai Yi, Guisheng Fan, Liang Hong
Protein Engineering with Lightweight Graph Denoising Neural Networks. Journal of chemical information and modeling 64 (9) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Yu Zhu, Jing Gu, Zhuoran Zhao, Ah Wing Edith Chan, Maria F Mojica, Andrea M Hujer, Robert A Bonomo, Shozeb M Haider
Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. Journal of chemical information and modeling 64 (9) (2024)
Krishnendu Sinha, Ipsita Basu, Zacharia Shah, Salim Shah, Suman Chakrabarty
Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction. Journal of chemical information and modeling 64 (9) (2024)
Moritz Walter, Samuel J Webb, Valerie J Gillet
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features. Journal of chemical information and modeling 64 (9) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Tzu-Hsien Yang
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. Journal of chemical information and modeling 64 (9) (2024)
Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi
Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model. Journal of chemical information and modeling 64 (9) (2024)
Maksim Kuznetsov, Fedor Ryabov, Roman S Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alexander Aliper, Daniil Polykovskiy
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework. Journal of chemical information and modeling 64 (9) (2024)
Pieter B Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M Kaiser
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. Journal of chemical information and modeling 64 (9) (2024)
Yu Zhu, Jing Gu, Zhuoran Zhao, Ah Wing Edith Chan, Maria F Mojica, Andrea M Hujer, Robert A Bonomo, Shozeb M Haider
Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. Journal of chemical information and modeling 64 (9) (2024)
Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huan-Xiang Liu, Ting-Jun Hou, Yu Kang
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. Journal of chemical information and modeling 64 (9) (2024)
Stefan Boresch
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. Journal of chemical information and modeling 64 (9) (2024)
Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R Houston
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening. Journal of chemical information and modeling 64 (9) (2024)
Hajime Shimakawa, Akiko Kumada, Masahiro Sato
Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties. Journal of chemical information and modeling 64 (9) (2024)
Otávio Luís de Santana, Daniel G Silva, Sidney R Santana
Solvate Suite : A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling. Journal of chemical information and modeling 64 (9) (2024)
Pengchao Zhang, Axel Tosello Gardini, Xuefei Xu, Michele Parrinello
Intramolecular and Water Mediated Tautomerism of Solvated Glycine. Journal of chemical information and modeling 64 (9) (2024)
Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R Houston
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening. Journal of chemical information and modeling 64 (9) (2024)
David Ferro-Costas, Pedro A Sánchez-Murcia, Antonio Fernandez-Ramos
Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation. Journal of chemical information and modeling 64 (9) (2024)
Marzieh Saeedimasine, Roja Rahmani, Alexander P Lyubartsev
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. Journal of chemical information and modeling 64 (9) (2024)
Maksim Kuznetsov, Fedor Ryabov, Roman S Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alexander Aliper, Daniil Polykovskiy
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework. Journal of chemical information and modeling 64 (9) (2024)
Zhengyue Zhang, Vojtěch Mlýnský, Miroslav Krepl, Jiřı Šponer, Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. Journal of chemical information and modeling 64 (9) (2024)
Stefan Boresch
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. Journal of chemical information and modeling 64 (9) (2024)
Daniel S Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C Felton, Alexei A Lapkin
ORDerly: Data Sets and Benchmarks for Chemical Reaction Data. Journal of chemical information and modeling 64 (9) (2024)
Marzieh Saeedimasine, Roja Rahmani, Alexander P Lyubartsev
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. Journal of chemical information and modeling 64 (9) (2024)
Stefan Boresch
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. Journal of chemical information and modeling 64 (9) (2024)
Yu Pang, Yihao Chen, Mujie Lin, Yanhong Zhang, Ji-Quan Zhang, Ling Wang
MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations. Journal of chemical information and modeling 64 (9) (2024)
Vincenzo Vigna, Tânia F G G Cova, Sandra C C Nunes, Alberto Canelas Pais, Emilia Sicilia
Machine Learning-Based Prediction of Reduction Potentials for Pt IV Complexes. Journal of chemical information and modeling 64 (9) (2024)
Ying Zheng, Nianhang Chen, Zhongju Ji, Qiongyu Ye, Pingping Huang, Xiaodie Chen, Guanghong Cui, Lixin Duan, Fan Zhang
Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site. Journal of chemical information and modeling 64 (9) (2024)
Moritz Walter, Samuel J Webb, Valerie J Gillet
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features. Journal of chemical information and modeling 64 (9) (2024)
Mueed Ur Rahman, Saira Bano, Xiaokun Hong, Ruo-Xu Gu, Hai-Feng Chen
Early Aggregation Mechanism of SOD1 28-38 Based on Force Field Parameter of 5-Cyano-Tryptophan. Journal of chemical information and modeling 64 (9) (2024)
Lina Zhao, Yanjiao Wang, Yi Zhang, Hao Chen, Fude Sun
Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane. Journal of chemical information and modeling 64 (9) (2024)
Daniel S Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C Felton, Alexei A Lapkin
ORDerly: Data Sets and Benchmarks for Chemical Reaction Data. Journal of chemical information and modeling 64 (9) (2024)
Daniel S Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C Felton, Alexei A Lapkin
ORDerly: Data Sets and Benchmarks for Chemical Reaction Data. Journal of chemical information and modeling 64 (9) (2024)
Sankar Maity, Somdev Pahari, Santanu Santra, Madhurima Jana
Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. Journal of chemical information and modeling 64 (9) (2024)
Koichi Handa, Saki Yoshimura, Michiharu Kageyama, Takeshi Iijima
Development of Novel Methods for QSAR Modeling by Machine Learning Repeatedly: A Case Study on Drug Distribution to Each Tissue. Journal of chemical information and modeling 64 (9) (2024)
Pieter B Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M Kaiser
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. Journal of chemical information and modeling 64 (9) (2024)
Tzu-Hsien Yang
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. Journal of chemical information and modeling 64 (9) (2024)
Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song
FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins. Journal of chemical information and modeling 64 (9) (2024)
Dulce C Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, Laura Domínguez
Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction. Journal of chemical information and modeling 64 (9) (2024)
Dhiman Ray, Sudip Das, Umberto Raucci
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. Journal of chemical information and modeling 64 (9) (2024)
Da-Zhou Li, Xin Xu, Jia-Heng Pan, Wei Gao, Shi-Rui Zhang
Image2InChI: Automated Molecular Optical Image Recognition. Journal of chemical information and modeling 64 (9) (2024)