Tingjun Hou

According to our database1, Tingjun Hou authored at least 98 papers between 1999 and 2022.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.

Timeline

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Bibliography

2022
Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes.
J. Cheminformatics, 2022

Root-aligned SMILES for Molecular Retrosynthesis Prediction.
CoRR, 2022

ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images.
Briefings Bioinform., 2022

Comprehensive assessment of deep generative architectures for de novo drug design.
Briefings Bioinform., 2022

Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning.
Briefings Bioinform., 2022

2021
Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning.
Nat. Mach. Intell., 2021

PROTAC-DB: an online database of PROTACs.
Nucleic Acids Res., 2021

CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors.
Nucleic Acids Res., 2021

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations.
J. Chem. Inf. Model., 2021

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions.
J. Cheminformatics, 2021

Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion.
J. Cheminformatics, 2021

The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.
J. Cheminformatics, 2021

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models.
J. Cheminformatics, 2021

MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction.
Briefings Bioinform., 2021

Identification of active molecules against Mycobacterium tuberculosis through machine learning.
Briefings Bioinform., 2021

PySmash: Python package and individual executable program for representative substructure generation and application.
Briefings Bioinform., 2021

Scopy: an integrated negative design python library for desirable HTS/VS database design.
Briefings Bioinform., 2021

ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds.
Briefings Bioinform., 2021

Improving structure-based virtual screening performance via learning from scoring function components.
Briefings Bioinform., 2021

Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules.
Briefings Bioinform., 2021

Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets.
Briefings Bioinform., 2021

Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method.
Briefings Bioinform., 2021

DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.
Briefings Bioinform., 2021

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?
Briefings Bioinform., 2021

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.
Briefings Bioinform., 2021

Beware of the generic machine learning-based scoring functions in structure-based virtual screening.
Briefings Bioinform., 2021

QSAR-assisted-MMPA to expand chemical transformation space for lead optimization.
Briefings Bioinform., 2021

BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study.
Briefings Bioinform., 2021

2020
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.
J. Chem. Inf. Model., 2020

Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays.
J. Chem. Inf. Model., 2020

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
J. Chem. Inf. Model., 2020

Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis.
J. Chem. Inf. Model., 2020

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning.
J. Cheminformatics, 2020

Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning.
Bioinform., 2020

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power.
Briefings Bioinform., 2020

2019
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
Nucleic Acids Res., 2019

Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery.
J. Chem. Inf. Model., 2019

ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.
J. Chem. Inf. Model., 2019

Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2019

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
Bioinform., 2019

2018
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products.
J. Chem. Inf. Model., 2018

Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator.
J. Chem. Inf. Model., 2018

Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays.
Genom. Proteom. Bioinform., 2018

2017
Comparative analyses of structural features and scaffold diversity for purchasable compound libraries.
J. Cheminformatics, 2017

HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
J. Cheminformatics, 2017

2016
ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling.
J. Cheminformatics, 2016

CaFE: a tool for binding affinity prediction using end-point free energy methods.
Bioinform., 2016

2015
Structure-Activity Relationships and Anti-inflammatory Activities of <i>N</i>-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors.
J. Chem. Inf. Model., 2015

Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models.
J. Chem. Inf. Model., 2015

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.
J. Chem. Inf. Model., 2015

2014
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape.
PLoS Comput. Biol., 2014

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility.
J. Chem. Inf. Model., 2014

MORT: a powerful foundational library for computational biology and CADD.
J. Cheminformatics, 2014

2013
Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors.
J. Chem. Inf. Model., 2013

Accelerated Conformational Entropy Calculations Using Graphic Processing Units.
J. Chem. Inf. Model., 2013

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures.
J. Chem. Inf. Model., 2013

Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design.
J. Chem. Inf. Model., 2013

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches.
J. Chem. Inf. Model., 2013

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches.
J. Chem. Inf. Model., 2013

Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling.
J. Chem. Inf. Model., 2013

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines.
J. Cheminformatics, 2013

Allosite: a method for predicting allosteric sites.
Bioinform., 2013

A GPU based Conformational Entropy Calculation Method.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

2012
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations.
J. Chem. Inf. Model., 2012

Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase.
J. Chem. Inf. Model., 2012

Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2012

Studies on the Interactions between β<sub>2</sub> Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2012

ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs.
J. Chem. Inf. Model., 2012

A rule-based algorithm for automatic bond type perception.
J. Cheminformatics, 2012

Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines.
J. Cheminformatics, 2012

2011
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations.
J. Chem. Inf. Model., 2011

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient.
J. Comput. Chem., 2011

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
J. Comput. Chem., 2011

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy.
Bioinform., 2011

2010
Computational Modeling Toward Understanding Agonist Binding on Dopamine 3.
J. Chem. Inf. Model., 2010

Drug and Drug Candidate Building Block Analysis.
J. Chem. Inf. Model., 2010

Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells.
J. Chem. Inf. Model., 2010

2009
Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas.
J. Chem. Inf. Model., 2009

2007
Development of Reliable Aqueous Solubility Models and Their Application in Druglike Analysis.
J. Chem. Inf. Model., 2007

ADME Evaluation in Drug Discovery, 8. The Prediction of Human Intestinal Absorption by a Support Vector Machine.
J. Chem. Inf. Model., 2007

ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules?
J. Chem. Inf. Model., 2007

ADME Evaluation in Drug Discovery, 7. Prediction of Oral Absorption by Correlation and Classification.
J. Chem. Inf. Model., 2007

On the detection of functionally coherent groups of protein domains with an extension to protein annotation.
BMC Bioinform., 2007

2006
Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain.
PLoS Comput. Biol., 2006

2005
New Born Radii Deriving Method for Generalized Born Model.
J. Chem. Inf. Model., 2005

2004
Some Basic Data Structures and Algorithms for Chemical Generic Programming.
J. Chem. Inf. Model., 2004

ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties.
J. Chem. Inf. Model., 2004

ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach.
J. Chem. Inf. Model., 2004

ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas [J. Chem. Inf. Comput. Sci. 1058-1067(2003)].
J. Chem. Inf. Model., 2004

ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors [J. Chem. Inf. Comput. Sci. 43, 2137-2152 (2003)]
J. Chem. Inf. Model., 2004

2003
Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies.
J. Chem. Inf. Comput. Sci., 2003

ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors.
J. Chem. Inf. Comput. Sci., 2003

ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas.
J. Chem. Inf. Comput. Sci., 2003

2002
A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs.
J. Chem. Inf. Comput. Sci., 2002

Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics.
J. Comput. Aided Mol. Des., 2002

2001
3D QSAR Analyses of Novel Tyrosine Kinase Inhibitors Based on Pharmacophore Alignment.
J. Chem. Inf. Comput. Sci., 2001

2000
Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis.
J. Chem. Inf. Comput. Sci., 2000

1999
Applications of Genetic Algorithms on the Structure-Activity Relationship Analysis of Some Cinnamamides.
J. Chem. Inf. Comput. Sci., 1999


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