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J. Chem. Inf. Model.
2004
2010
2018
2024
2004
2024
Keyphrases
Publications
volume 64, number 8, 2024
Teng-Zhi Long
,
Dejun Jiang
,
Shao-Hua Shi
,
You-Chao Deng
,
Wen-Xuan Wang
,
Dong-Sheng Cao
Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence.
J. Chem. Inf. Model.
64 (8) (2024)
Damla Ovek
,
Ozlem Keskin
,
Attila Gürsoy
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations.
J. Chem. Inf. Model.
64 (8) (2024)
Martin Priessner
,
Richard J. Lewis
,
Magnus J. Johansson
,
Jonathan M. Goodman
,
Jon Paul Janet
,
Anna Tomberg
HSQC Spectra Simulation and Matching for Molecular Identification.
J. Chem. Inf. Model.
64 (8) (2024)
Rafael Giordano Viegas
,
Ingrid B. S. Martins
,
Murilo Nogueira Sanches
,
Antonio B. Oliveira Junior
,
Juliana B. de Camargo
,
Fernando V. Paulovich
,
Vitor B. P. Leite
ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization.
J. Chem. Inf. Model.
64 (8) (2024)
Tengyu Xie
,
Jing Huang
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?
J. Chem. Inf. Model.
64 (8) (2024)
Hongyan Chen
,
Dongxue Yan
,
Jie Sun
,
Meng Zhou
Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning.
J. Chem. Inf. Model.
64 (8) (2024)
Jiamin Chang
,
Xiaoyu Fan
,
Boxue Tian
DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation.
J. Chem. Inf. Model.
64 (8) (2024)
Zhe Su
,
Yiying Tong
,
Guo-Wei Wei
Hodge Decomposition of Single-Cell RNA Velocity.
J. Chem. Inf. Model.
64 (8) (2024)
Satyabrata Majumder
,
Giuseppe Deganutti
,
Ludovico Pipitò
,
Dwaipayan Chaudhuri
,
Joyeeta Datta
,
Kalyan Giri
Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling.
J. Chem. Inf. Model.
64 (8) (2024)
David C. Williams
,
Neil Inala
Physics-Informed Generative Model for Drug-like Molecule Conformers.
J. Chem. Inf. Model.
64 (8) (2024)
Ander Francisco Pereira
,
Leandro Martínez
Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A.
J. Chem. Inf. Model.
64 (8) (2024)
Felipe L. Oliveira
,
Pierre M. Esteves
pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular Approach.
J. Chem. Inf. Model.
64 (8) (2024)
Maria José Tenorio
,
Miguel Á. González
,
Julia D. Magdaleno
,
Inmaculada Suárez
,
Baudilio Coto
= (293.15 to 343.15) K. Experiment and Modeling.
J. Chem. Inf. Model.
64 (8) (2024)
Hazem Mslati
,
Francesco Gentile
,
Mohit Pandey
,
Fuqiang Ban
,
Artem Cherkasov
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs.
J. Chem. Inf. Model.
64 (8) (2024)
Joel Graef
,
Christiane Ehrt
,
Thorben Reim
,
Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces.
J. Chem. Inf. Model.
64 (8) (2024)
Yu Zou
,
Lulu Guan
,
Jingwang Tan
,
Bote Qi
,
Yunxiang Sun
,
Fengjuan Huang
,
Qingwen Zhang
Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats.
J. Chem. Inf. Model.
64 (8) (2024)
Jiaojiao Wang
,
Ting Ren
,
Guohui Sun
,
Na Zhang
,
Lijiao Zhao
,
Rugang Zhong
Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation.
J. Chem. Inf. Model.
64 (8) (2024)
volume 64, number 9, 2024
Mueed Ur Rahman
,
Saira Bano
,
Xiaokun Hong
,
Ruo-Xu Gu
,
Hai-Feng Chen
Based on Force Field Parameter of 5-Cyano-Tryptophan.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Dhiman Ray
,
Sudip Das
,
Umberto Raucci
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations.
J. Chem. Inf. Model.
64 (9) (2024)
Maksim Kuznetsov
,
Fedor Ryabov
,
Roman Schutski
,
Rim Shayakhmetov
,
Yen-Chu Lin
,
Alex Aliper
,
Daniil Polykovskiy
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework.
J. Chem. Inf. Model.
64 (9) (2024)
Da-zhou Li
,
Xin Xu
,
Jia-heng Pan
,
Wei Gao
,
Shi-rui Zhang
Image2InChI: Automated Molecular Optical Image Recognition.
J. Chem. Inf. Model.
64 (9) (2024)
Vincenzo Vigna
,
Tânia F. G. G. Cova
,
Sandra C. C. Nunes
,
A. A. C. C. Pais
,
Emilia Sicilia
Complexes.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Marzieh Saeedimasine
,
Roja Rahmani
,
Alexander P. Lyubartsev
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning.
J. Chem. Inf. Model.
64 (9) (2024)
Sankar Maity
,
Somdev Pahari
,
Santanu Santra
,
Madhurima Jana
Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations.
J. Chem. Inf. Model.
64 (9) (2024)
Stefan Boresch
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations.
J. Chem. Inf. Model.
64 (9) (2024)
Yu Zhu
,
Jing Gu
,
Zhuoran Zhao
,
A. W. 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.
J. Chem. Inf. Model.
64 (9) (2024)
David Ferro-Costas
,
Pedro A. Sánchez-Murcia
,
Antonio Fernández-Ramos
Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation.
J. Chem. Inf. Model.
64 (9) (2024)
Dulce C. Guzmán-Ocampo
,
Rodrigo Aguayo-Ortiz
,
Laura Dominguez
Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Sergey Gorelov
,
Anatoly Titov
,
Olga Tolicheva
,
Andrey Konevega
,
Alexey Shvetsov
DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Pieter Buys 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.
J. Chem. Inf. Model.
64 (9) (2024)
Haopeng Ai
,
Deyin Wu
,
Huihao Zhou
,
Jun Xu
,
Qiong Gu
Small-Molecule 3D Structure Predictor with Graph Attention Networks.
J. Chem. Inf. Model.
64 (9) (2024)
Shukai Gu
,
Yuwei Yang
,
Yihao Zhao
,
Jiayue Qiu
,
Xiaorui Wang
,
Henry Hoi Yee Tong
,
Liwei Liu
,
Xiaozhe Wan
,
Huanxiang Liu
,
Tingjun Hou
,
Yu Kang
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios.
J. Chem. Inf. Model.
64 (9) (2024)
Otávio L. Santana
,
Daniel G. Silva
,
Sidney R. Santana
: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Tzu-Hsien Yang
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning.
J. Chem. Inf. Model.
64 (9) (2024)
Paige E. Bowling
,
Saswata Dasgupta
,
John M. Herbert
Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Zhengyue Zhang
,
Vojtech Mlýnský
,
Miroslav Krepl
,
Jirí Sponer
,
Petr Stadlbauer
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.
J. Chem. Inf. Model.
64 (9) (2024)
Hajime Shimakawa
,
Akiko Kumada
,
Masahiro Sato
Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Yu Pang
,
Yihao Chen
,
Mujie Lin
,
Yanhong Zhang
,
Jiquan Zhang
,
Ling Wang
MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (9) (2024)
Moritz Walter
,
Samuel J. Webb
,
Valerie J. Gillet
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features.
J. Chem. Inf. Model.
64 (9) (2024)
Pengchao Zhang
,
Axel Tosello Gardini
,
Xuefei Xu
,
Michele Parrinello
Intramolecular and Water Mediated Tautomerism of Solvated Glycine.
J. Chem. Inf. Model.
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.
J. Chem. Inf. Model.
64 (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.
J. Chem. Inf. Model.
64 (9) (2024)