Jianfeng Pei

发表

Automatic Retrosynthetic Pathway Planning Using Template-free Models

Kangjie Lin, Youjun Xu, Jianfeng Pei, 2019, 1906.02308.

Systems biology brings new dimensions for structure-based drug design.

Jianfeng Pei, L. Lai, Xiaomin Ma, 2014, Journal of the American Chemical Society.

Computational Identification of a New Binding Site in Influenza Virus Hemagglutinin for Membrane Fusion Inhibitors

Jianfeng Pei, L. Zhang, Lidan Sun, 2013, Chemical biology & drug design.

H2A.Z facilitates licensing and activation of early replication origins

Jianfeng Pei, R. Margueron, Tongqing Li, 2019, Nature.

Binding site detection and druggability prediction of protein targets for structure-based drug design.

Jianfeng Pei, L. Lai, Yaxia Yuan, 2013, Current pharmaceutical design.

Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues

Jianfeng Pei, L. Lai, Weilin Zhang, 2017, J. Chem. Inf. Model..

Transfer Learning for Drug Discovery.

Youjun Xu, Jianfeng Pei, L. Lai, 2020, Journal of medicinal chemistry.

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

Jianfeng Pei, Shuo Gu, 2017, Evidence-based complementary and alternative medicine : eCAM.

Understanding molecular mechanisms of traditional Chinese medicine for the treatment of influenza viruses infection by computational approaches.

Jianfeng Pei, L. Lai, Shuo Gu, 2013, Molecular bioSystems.

Understanding traditional Chinese medicine anti-inflammatory herbal formulae by simulating their regulatory functions in the human arachidonic acid metabolic network.

Jianfeng Pei, L. Lai, Shuo Gu, 2013, Molecular bioSystems.

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

Jianfeng Pei, Tanlin Sun, Linjie Zhao, 2015, Proceedings of the National Academy of Sciences.

PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking

Luhua Lai, Jianfeng Pei, Zhenming Liu, 2006, Proteins.

Quaternary structure, substrate selectivity and inhibitor design for SARS 3C-like proteinase.

Y. Liu, Jianfeng Pei, L. Lai, 2006, Current pharmaceutical design.

Estimating protein–ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation

Luhua Lai, Jianfeng Pei, Jiaju Zhou, 2004, Proteins.

CAVITY: Mapping the Druggable Binding Site

Jianfeng Pei, L. Lai, Weilin Zhang, 2015 .

A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures.

Luhua Lai, Jianfeng Pei, Jianfeng Pei, 2007, Biophysical journal.

Prediction of liquid-liquid phase separation proteins using machine learning

Youjun Xu, Jianfeng Pei, L. Lai, 2019, bioRxiv.

14-3-3ζ Interacts with Stat3 and Regulates Its Constitutive Activation in Multiple Myeloma Cells

Jianfeng Pei, Fangjin Chen, Mingkun Yang, 2012, PloS one.

Effects of Sulfate Residues on the Interaction of Basic Fibroblast Growth Factor with Heparin Evaluated by Combination of Computer Modeling and Surface Plasmon Resonance methods

Jianfeng Pei, Z. Fan, Yapeng Chao, 2013 .

A combined computational and experimental strategy identifies mutations conferring resistance to drugs targeting the BCR-ABL fusion protein

Jianfeng Pei, L. Lai, Jinxin Liu, 2020, Communications Biology.

Gastrodin interaction with human fibrinogen: anticoagulant effects and binding studies.

Jianfeng Pei, F. Liu, K. Li, 2006, Chemistry.

MolMiner: You only look once for chemical structure recognition

Youjun Xu, Jianfeng Pei, Weilin Zhang, 2022, J. Chem. Inf. Model..

3D‐QSAR and Receptor Modeling of Tyrosine Kinase Inhibitors with Flexible Atom Receptor Model (FLARM).

Jianfeng Pei, Jiaju Zhou, T. Peng, 2003 .

Innovating Chinese Herbal Medicine: From Traditional Health Practice to Scientific Drug Discovery

Jianfeng Pei, Shuo Gu, 2017, Front. Pharmacol..

A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification

Jianfeng Pei, L. Lai, A. Bender, 2007, J. Chem. Inf. Model..

Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions

Jianfeng Pei, D. Czajkowsky, Fang Wang, 2022, bioRxiv.

Synergistic and Antagonistic Drug Combinations Depend on Network Topology

Luhua Lai, Jianfeng Pei, Ning Yin, 2014, PloS one.

Cadmium modulates hematopoietic stem and progenitor cells and skews toward myelopoiesis in mice.

Jianfeng Pei, Zhijun Zhou, P. Xue, 2016, Toxicology and applied pharmacology.

A NR2E1‐interacting peptide of LSD1 inhibits the proliferation of brain tumour initiating cells

Jianfeng Pei, P. Jeffrey, K. Swaminathan, 2021, Cell proliferation.

A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels.

Jianfeng Pei, L. Lai, N. Yin, 2013, Molecular bioSystems.

Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models

Jianfeng Pei, L. Lai, Yibo Li, 2022, J. Chem. Inf. Model..

Biosynthesis, Purification, and Substrate Specificity of Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase

Luhua Lai, Jianfeng Pei, Ying Liu, 2004, Journal of Biological Chemistry.

Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors.

Luhua Lai, Jianfeng Pei, Ying Liu, 2006, Journal of medicinal chemistry.

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database

Xia Wang, Weilin Zhang, Luhua Lai, 2017, Nucleic Acids Res..

Sequence-based prediction of protein protein interaction using a deep-learning algorithm

Luhua Lai, Bo Zhou, Jianfeng Pei, 2017, BMC Bioinformatics.

LigBuilder V3: A Multi-Target de novo Drug Design Approach

Luhua Lai, Jianfeng Pei, Yaxia Yuan, 2020, Frontiers in Chemistry.

A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2

Youjun Xu, Luhua Lai, Qi Sun, 2020, bioRxiv.

Computational Multitarget Drug Design

Weilin Zhang, Luhua Lai, Jianfeng Pei, 2017, J. Chem. Inf. Model..

Discovering potent small molecule inhibitors of cyclophilin A using de novo drug design approach.

Luhua Lai, Jianfeng Pei, Jin Huang, 2009, Journal of medicinal chemistry.

Deep Learning for Drug-Induced Liver Injury

Luhua Lai, Jianfeng Pei, Youjun Xu, 2015, J. Chem. Inf. Model..

Structure-based de novo drug design using 3D deep generative models

Jianfeng Pei, L. Lai, Yibo Li, 2021, Chemical science.

A combined computational and experimental strategy identifies mutations conferring resistance to drugs targeting the BCR-ABL fusion protein

Jianfeng Pei, L. Lai, Jinxin Liu, 2020, Communications Biology.

iDrug: a web-accessible and interactive drug discovery and design platform

Xia Wang, Luhua Lai, Feng Yang, 2014, Journal of Cheminformatics.

CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction

Weilin Zhang, Luhua Lai, Jianfeng Pei, 2018, Nucleic Acids Res..

Sequence-based prediction of protein protein interaction using a deep-learning algorithm

Jianfeng Pei, L. Lai, Tanlin Sun, 2017, BMC Bioinformatics.

Novel Inhibitors of Toxin HipA Reduce Multidrug Tolerant Persisters.

Luhua Lai, Jianfeng Pei, Ning Yin, 2016, ACS medicinal chemistry letters.

Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis

Jianfeng Pei, D. Czajkowsky, J. Xie, 2018, EBioMedicine.

3D-QSAR studies on tripeptide aldehyde inhibitors of proteasome using CoMFA and CoMSIA methods.

Jianfeng Pei, Yong Zhu, Zhen-ming Liu, 2006, Bioorganic & medicinal chemistry.

A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins

Jakub W. Wojciechowski, Jianfeng Pei, P. Roy, 2022, bioRxiv.

Virtual Screening of Novel Noncovalent Inhibitors for SARS-CoV 3C-like Proteinase

Hao Chen, Ying Liu, Lei Shi, 2005, J. Chem. Inf. Model..

Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

Jianfeng Pei, Youjun Xu, Luhua Lai, 2017, J. Chem. Inf. Model..

Regulation of interferon production as a potential strategy for COVID-19 treatment

Jianfeng Pei, Xiaobing Deng, Xiaoyu Yu, 2020, 2003.00751.

Analysis of protein features and machine learning algorithms for prediction of druggable proteins

Luhua Lai, Jianfeng Pei, Tanlin Sun, 2018, Quantitative Biology.

Cabazitaxel suppresses colorectal cancer cell growth via enhancing the p53 antitumor pathway

Jianfeng Pei, Wen Zhang, Yongjun Zhang, 2021, FEBS open bio.

De Novo Design of Multitarget Ligands with an Iterative Fragment-Growing Strategy

Ying Liu, Xinyi Chen, Luhua Lai, 2014, J. Chem. Inf. Model..

Structure-based de novo drug design using 3D deep generative models pdf

Luhua Lai, Jianfeng Pei, Yibo Li, 2021, Chemical science.

Deep learning for molecular generation.

Jianfeng Pei, Youjun Xu, Kangjie Lin, 2019, Future medicinal chemistry.

Molecular dynamic analysis of mutant Y195I α-cyclodextrin glycosyltransferase with switched product specificity from α-cyclodextrin to γ-cyclodextrin

Jianfeng Pei, Fangjin Chen, Yapeng Chao, 2015, Journal of Molecular Modeling.

LigBuilder 2: A Practical de Novo Drug Design Approach

Luhua Lai, Yaxia Yuan, Jianfeng Pei, 2011, J. Chem. Inf. Model..

CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome

Youjun Xu, Jianfeng Pei, L. Lai, 2022, bioRxiv.

A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity

Jianfeng Pei, Yushan Zhu, Jianfeng Pei, 2010, Journal of molecular modeling.

QuoteTarget: A sequence‐based transformer protein language model to identify potentially druggable protein targets

Minghua Deng, Youjun Xu, Jianfeng Pei, 2022, Protein science : a publication of the Protein Society.

Improving the Quality of 3D-QSAR by Using Flexible-Ligand Receptor Models

Hao Chen, Bin Shen, Qi Wang, 2005, J. Chem. Inf. Model..

Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network.

Jianfeng Pei, Youjun Xu, Luhua Lai, 2018, Molecular pharmaceutics.

Crystal Structure Analysis of a Recombinant Predicted Acetamidase/Formamidase from the Thermophile Thermoanaerobacter tengcongensis

Jianfeng Pei, L. Lai, M. Kusunoki, 2011, The Protein Journal.

Discovery of multitarget inhibitors by combining molecular docking with common pharmacophore matching.

Luhua Lai, Jianfeng Pei, Ying Liu, 2008, Journal of medicinal chemistry.

Prediction of Drug-Likeness Using Deep Autoencoder Neural Networks

Luhua Lai, Jianfeng Pei, Qiwan Hu, 2018, Front. Genet..

Computational Chemical Synthesis Analysis and Pathway Design

Luhua Lai, Jianfeng Pei, Fan Feng, 2018, Front. Chem..

miDruglikeness: Subdivisional Drug-Likeness Prediction Models Using Active Ensemble Learning Strategies

Youjun Xu, Jianfeng Pei, L. Lai, 2022, Biomolecules.

Efficient molecular encoders for virtual screening.

Shiwei Wang, Jianfeng Pei, Youjun Xu, 2019, Drug discovery today. Technologies.

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

Jianfeng Pei, Tanlin Sun, Linjie Zhao, 2015, Proceedings of the National Academy of Sciences.

Multiple Target Drug Design Using LigBuilder 3.

Jianfeng Pei, L. Lai, Xiaoyu Qing, 2021, Methods in molecular biology.

Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

Luhua Lai, Jianfeng Pei, Youjun Xu, 2017, J. Chem. Inf. Model..

Accelerating Discovery of Novel and Bioactive Ligands With Pharmacophore-Informed Generative Models

Youjun Xu, Jianfeng Pei, Jianhang Zhang, 2024, 2401.01059.

In silico protein function prediction: the rise of machine learning-based approaches

Jianfeng Pei, Zhonghui Gu, Jiaxiao Chen, 2023, Medical review.

Prediction of liquid–liquid phase separating proteins using machine learning

Youjun Xu, Jianfeng Pei, L. Lai, 2022, BMC Bioinformatics.

DeepRLI: A Multi-objective Framework for Universal Protein--Ligand Interaction Prediction

Jianfeng Pei, Shiwei Wang, Luhua Lai, 2024, 2401.10806.

Exploring the Interaction Mechanism of Desmethyl-broflanilide in Insect GABA Receptors and Screening Potential Antagonists by In Silico Simulations.

Jianfeng Pei, Xiaogang Luo, Genyan Liu, 2020, Journal of agricultural and food chemistry.

Automatic retrosynthetic route planning using template-free models

Jianfeng Pei, Youjun Xu, Kangjie Lin, 2020, Chemical science.

Challenging Complexity with Simplicity: Rethinking the Role of Single-Step Models in Computer-Aided Synthesis Planning.

Kangjie Lin, Jianfeng Pei, L. Lai, 2024, Journal of chemical information and modeling.

LigBuilder 2: A Practical de Novo Drug Design Approach

Jianfeng Pei, L. Lai, Yaxia Yuan, 2011, J. Chem. Inf. Model..