List of works - Yu Zong Chen

A Global Characterization and Identification of Multifunctional Enzymes ⬇️

scientific article published on June 18, 2012

A Two-Step Target Binding and Selectivity Support Vector Machines Approach for Virtual Screening of Dopamine Receptor Subtype-Selective Ligands ⬇️

scientific article published on June 15, 2012

A benchmarking study on virtual ligand screening against homology models of human GPCRs

scientific article published on 23 September 2018

A preclinical evaluation of SKLB261, a multikinase inhibitor of EGFR/Src/VEGFR2, as a therapeutic agent against pancreatic cancer

scientific article published on 17 December 2014

A prediction model of drug-induced ototoxicity developed by an optimal support vector machine (SVM) method

scientific article published on 17 May 2014

A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P

scientific article

Advances in machine learning prediction of toxicological properties and adverse drug reactions of pharmaceutical agents

scientific article published on May 2008

An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability ⬇️

scientific article published on July 15, 2011

Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors ⬇️

scientific article published on October 1, 2012

Antiproliferative activities of the second-generation antipsychotic drug sertindole against breast cancers with a potential application for treatment of breast-to-brain metastases

scientific article published in Scientific Reports

Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.

scientific article published on 8 January 2018

BSFINDER: finding binding sites of HCV proteins using a support vector machine

scientific article published on January 2009

CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering

scientific article

CMAUP: a database of collective molecular activities of useful plants

article

Calcyclin-binding protein inhibits proliferation, tumorigenicity, and invasion of gastric cancer

scientific article published on December 2007

Celecoxib could reverse the hypoxia-induced Angiopoietin-2 upregulation in gastric cancer

scientific article published on 9 December 2005

Cellular prion protein promotes proliferation and G1/S transition of human gastric cancer cells SGC7901 and AGS.

scientific article published on 4 April 2007

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

scientific article published on 30 December 2017

Clustered distribution of natural product leads of drugs in the chemical space as influenced by the privileged target-sites

scientific article published on 20 March 2015

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting ⬇️

scientific article published on July 18, 2011

Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs

scientific article published on 03 October 2015

Combining kinase inhibitors for optimally co-targeting cancer and drug escape by exploitation of drug target promiscuities

scientific article published on 15 September 2020

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries

scientific article published on May 2009

Computational characterization of the selective inhibition of human norepinephrine and serotonin transporters by an escitalopram scaffold

scientific article published on 01 November 2018

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

scientific article published on 16 February 2018

Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties

scientific article published on 23 March 2006

Database and Bioinformatics Studies of Probiotics.

scientific article published on 20 July 2017

Decitabine of reduced dosage in Chinese patients with myelodysplastic syndrome: a retrospective analysis

scientific article

Description of base motion and role of excitations in the melting of poly(dG).poly(dC)

scientific article published on October 1, 1992

Design, synthesis and evaluation of acridine derivatives as multi-target Src and MEK kinase inhibitors for anti-tumor treatment

scientific article published on 8 December 2015

Detection of Hepatitis B Virus Large Surface Protein Using a Time-Resolved Immunofluorometric Assay.

scientific article published on 2 October 2014

Development and experimental test of support vector machines virtual screening method for searching Src inhibitors from large compound libraries ⬇️

scientific article published on November 23, 2012

Development of Ligand-based Big Data Deep Neural Network Models for Virtual Screening of Large Compound Libraries

scientific article published on 08 June 2018

Differentiating Physicochemical Properties between Addictive and Nonaddictive ADHD Drugs Revealed by Molecular Dynamics Simulation Studies.

scientific article published on 30 May 2017

Differentiating physicochemical properties between NDRIs and sNRIs clinically important for the treatment of ADHD.

scientific article published on 27 July 2017

Discovery of 1-(3-aryl-4-chlorophenyl)-3-(p-aryl)urea derivatives against breast cancer by inhibiting PI3K/Akt/mTOR and Hedgehog signalings.

scientific article published on 6 October 2017

Discovery of indolylpiperazinylpyrimidines with dual-target profiles at adenosine A2A and dopamine D2 receptors for Parkinson's disease treatment

scientific article

Discovery of novel dual VEGFR2 and Src inhibitors using a multistep virtual screening approach

scientific article

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

scientific article published on 26 June 2018

Drug discovery prospect from untapped species: indications from approved natural product drugs

scientific article

Drug sales confirm clinical advantage of multi-target inhibition of drug escapes by anticancer kinase inhibitors

scientific article published on 13 November 2018

EMMPRIN Is an Independent Negative Prognostic Factor for Patients with Astrocytic Glioma ⬇️

scientific article published on March 13, 2013

Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries

scientific article

Effect of training datasets on support vector machine prediction of protein-protein interactions

scientific article published in March 2005

Elevated Expression of Carboxy-Terminal Modulator Protein (CTMP) Aggravates Brain Ischemic Injury in Diabetic db/db Mice

scientific article published on 9 May 2016

Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates

scientific article published on October 1, 1992

Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations

scientific article published in 2023

Exploration of (S)-3-aminopyrrolidine as a potentially interesting scaffold for discovery of novel Abl and PI3K dual inhibitors ⬇️

scientific article published on January 21, 2011

Exploration of N-(2-aminoethyl)piperidine-4-carboxamide as a potential scaffold for development of VEGFR-2, ERK-2 and Abl-1 multikinase inhibitor ⬇️

scientific article published on July 20, 2013

Exploration of acridine scaffold as a potentially interesting scaffold for discovering novel multi-target VEGFR-2 and Src kinase inhibitors ⬇️

scientific article published on June 1, 2011

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

scientific article published on 9 March 2018

HEROD: a human ethnic and regional specific omics database

scientific article

HIT: linking herbal active ingredients to targets ⬇️

scientific article published on November 21, 2010

Human mitochondrial Mrs2 protein promotes multidrug resistance in gastric cancer cells by regulating p27, cyclin D1 expression and cytochrome C release

scientific article

Human ribosomal protein S13 promotes gastric cancer growth through down-regulating p27(Kip1).

scientific article published on February 2011

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

scientific article published on 8 January 2016

Identifying Novel Type ZBGs and Nonhydroxamate HDAC Inhibitors Through a SVM Based Virtual Screening Approach

scientific article

In silico prediction of adverse drug reactions and toxicities based on structural, biological and clinical data

scientific article

Inhibition of epidermal growth factor receptor tyrosine kinase by chalcone derivatives ⬇️

scientific article published on December 17, 2001

Internet resources for proteins associated with drug therapeutic effects, adverse reactions and ADME.

scientific article

Molecular basis of therapeutic approaches to gastric cancer

scientific article published on January 2009

Multitarget inhibitors derived from crosstalk mechanism involving VEGFR2.

scientific article

NOREVA: normalization and evaluation of MS-based metabolomics data

scientific article

NPASS: natural product activity and species source database for natural product research, discovery and tool development

scientific article

Nature's contribution to today's pharmacopeia

scientific article published in October 2014

Neighbor communities in drug combination networks characterize synergistic effect ⬇️

scientific article published on October 30, 2012

Neuroprotective gases--fantasy or reality for clinical use?

scientific article published on 15 January 2014

Nicotine-induced neuroprotection against ischemic injury involves activation of endocannabinoid system in rats

scientific article published on 29 November 2012

Novel synthetic acridine derivatives as potent DNA-binding and apoptosis-inducing antitumor agents ⬇️

scientific article published on May 16, 2013

Overexpressed CacyBP/SIP leads to the suppression of growth in renal cell carcinoma

scientific article

Pharmacological relationships and ligand discovery of G protein-coupled receptors revealed by simultaneous ligand and receptor clustering

scientific article published on 11 July 2017

Phthalimide conjugations for the degradation of oncogenic PI3K.

scientific article published on 26 March 2018

Physicochemical Profiles of the Marketed Agrochemicals and Clues for Agrochemical Lead Discovery and Screening Library Development

scientific article

Polymorphisms in the vitamin D receptor gene and risk of primary biliary cirrhosis: a meta-analysis

scientific article published on April 2014

Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway

scientific article published on 19 January 2017

Predicting Targeted Polypharmacology for Drug Repositioning and Multi- Target Drug Discovery ⬇️

scientific article published on January 1, 2013

Predicting the Enzymatic Hydrolysis Half-lives of New Chemicals Using Support Vector Regression Models Based on Stepwise Feature Elimination

scientific article published on 19 June 2017

Prediction of RNA-binding proteins from primary sequence by a support vector machine approach

scientific article

Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines

scientific article

Prediction of human major histocompatibility complex class II binding peptides by continuous kernel discrimination method ⬇️

scientific article published on November 30, 2011

Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach ⬇️

scientific article published on January 1, 2001

Prognostic relevance of miR-137 and its liver microenvironment regulatory target gene AFM in hepatocellular carcinoma

scientific article published on 06 December 2018

RUNX3 Mediates Suppression of Tumor Growth and Metastasis of Human CCRCC by Regulating Cyclin Related Proteins and TIMP-1 ⬇️

scientific article published on March 22, 2012

Recombinant human thioredoxin-1 promotes neurogenesis and facilitates cognitive recovery following cerebral ischemia in mice

scientific article

Revealing vilazodone's binding mechanism underlying its partial agonism to the 5-HT1A receptor in the treatment of major depressive disorder

scientific article published on 23 October 2017

Runx3 suppresses gastric cancer metastasis through inactivation of MMP9 by upregulation of TIMP-1.

scientific article published on 21 June 2011

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

scientific article

Salt-dependent stability of poly(dG).poly(dC) with potential of mean force Coulomb interactions

scientific article published on August 1, 1992

Simultaneous Quantification of Anticardiolipin IgG and IgM by Time Resolved Fluoroimmunoassay

scientific article

Suppression of the dual-specificity phosphatase MKP-1 enhances HIF-1 trans-activation and increases expression of EPO.

scientific article published on December 2003

The Assessment of the Readiness of Molecular Biomarker-Based Mobile Health Technologies for Healthcare Applications

scientific article

The Opening of a Single Base Without Perturbations of Neighboring Nucleotides: A Study on Crystal B-DNA duplex d(CGCGAATTCGCG)2 ⬇️

scientific article published on 01 February 1998

The Role of SUMO-Conjugating Enzyme Ubc9 in the Neuroprotection of Isoflurane Preconditioning Against Ischemic Neuronal Injury

scientific article published on 25 June 2014

The Therapeutic Target Database: an internet resource for the primary targets of approved, clinical trial and experimental drugs

scientific article published on 28 May 2011

The role of a minor groove spine of hydration in stabilizing poly(dA). poly(dT) against fuctuational interbase H-bond disruption in the premelting temperature regime ⬇️

scientific article published on February 11, 1992

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery ⬇️

scientific article published on September 24, 2011

Therapeutic target database update 2014: a resource for targeted therapeutics

scientific article

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

scientific article

Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics

scientific article published on 13 November 2017

Towards cheminformatics-based estimation of drug therapeutic index: Predicting the protective index of anticonvulsants using a new quantitative structure-index relationship approach

scientific article published on 19 May 2016

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence ⬇️

scientific article published on May 23, 2011

What Contributes to Serotonin-Norepinephrine Reuptake Inhibitors' Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation.

scientific article

What does it take to synergistically combine sub-potent natural products into drug-level potent combinations?

scientific article

p75 neurotrophin receptor suppresses the proliferation of human gastric cancer cells

scientific article published on June 2007

List of works by Yu Zong Chen

A Global Characterization and Identification of Multifunctional Enzymes ⬇️

A Two-Step Target Binding and Selectivity Support Vector Machines Approach for Virtual Screening of Dopamine Receptor Subtype-Selective Ligands ⬇️

A benchmarking study on virtual ligand screening against homology models of human GPCRs

A preclinical evaluation of SKLB261, a multikinase inhibitor of EGFR/Src/VEGFR2, as a therapeutic agent against pancreatic cancer

A prediction model of drug-induced ototoxicity developed by an optimal support vector machine (SVM) method

A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P

Advances in machine learning prediction of toxicological properties and adverse drug reactions of pharmaceutical agents

An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability ⬇️

Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors ⬇️

Antiproliferative activities of the second-generation antipsychotic drug sertindole against breast cancers with a potential application for treatment of breast-to-brain metastases

Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.

BSFINDER: finding binding sites of HCV proteins using a support vector machine

CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering

CMAUP: a database of collective molecular activities of useful plants

Calcyclin-binding protein inhibits proliferation, tumorigenicity, and invasion of gastric cancer

Celecoxib could reverse the hypoxia-induced Angiopoietin-2 upregulation in gastric cancer

Cellular prion protein promotes proliferation and G1/S transition of human gastric cancer cells SGC7901 and AGS.

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

Clustered distribution of natural product leads of drugs in the chemical space as influenced by the privileged target-sites

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting ⬇️

Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs

Combining kinase inhibitors for optimally co-targeting cancer and drug escape by exploitation of drug target promiscuities

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries

Computational characterization of the selective inhibition of human norepinephrine and serotonin transporters by an escitalopram scaffold

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties

Database and Bioinformatics Studies of Probiotics.

Decitabine of reduced dosage in Chinese patients with myelodysplastic syndrome: a retrospective analysis

Description of base motion and role of excitations in the melting of poly(dG).poly(dC)

Design, synthesis and evaluation of acridine derivatives as multi-target Src and MEK kinase inhibitors for anti-tumor treatment

Detection of Hepatitis B Virus Large Surface Protein Using a Time-Resolved Immunofluorometric Assay.

Development and experimental test of support vector machines virtual screening method for searching Src inhibitors from large compound libraries ⬇️

Development of Ligand-based Big Data Deep Neural Network Models for Virtual Screening of Large Compound Libraries

Differentiating Physicochemical Properties between Addictive and Nonaddictive ADHD Drugs Revealed by Molecular Dynamics Simulation Studies.

Differentiating physicochemical properties between NDRIs and sNRIs clinically important for the treatment of ADHD.

Discovery of 1-(3-aryl-4-chlorophenyl)-3-(p-aryl)urea derivatives against breast cancer by inhibiting PI3K/Akt/mTOR and Hedgehog signalings.

Discovery of indolylpiperazinylpyrimidines with dual-target profiles at adenosine A2A and dopamine D2 receptors for Parkinson's disease treatment

Discovery of novel dual VEGFR2 and Src inhibitors using a multistep virtual screening approach

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

Drug discovery prospect from untapped species: indications from approved natural product drugs

Drug sales confirm clinical advantage of multi-target inhibition of drug escapes by anticancer kinase inhibitors

EMMPRIN Is an Independent Negative Prognostic Factor for Patients with Astrocytic Glioma ⬇️

Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries

Effect of training datasets on support vector machine prediction of protein-protein interactions

Elevated Expression of Carboxy-Terminal Modulator Protein (CTMP) Aggravates Brain Ischemic Injury in Diabetic db/db Mice

Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates

Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations

Exploration of (S)-3-aminopyrrolidine as a potentially interesting scaffold for discovery of novel Abl and PI3K dual inhibitors ⬇️

Exploration of N-(2-aminoethyl)piperidine-4-carboxamide as a potential scaffold for development of VEGFR-2, ERK-2 and Abl-1 multikinase inhibitor ⬇️

Exploration of acridine scaffold as a potentially interesting scaffold for discovering novel multi-target VEGFR-2 and Src kinase inhibitors ⬇️

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

HEROD: a human ethnic and regional specific omics database

HIT: linking herbal active ingredients to targets ⬇️

Human mitochondrial Mrs2 protein promotes multidrug resistance in gastric cancer cells by regulating p27, cyclin D1 expression and cytochrome C release

Human ribosomal protein S13 promotes gastric cancer growth through down-regulating p27(Kip1).

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

Identifying Novel Type ZBGs and Nonhydroxamate HDAC Inhibitors Through a SVM Based Virtual Screening Approach

In silico prediction of adverse drug reactions and toxicities based on structural, biological and clinical data

Inhibition of epidermal growth factor receptor tyrosine kinase by chalcone derivatives ⬇️

Internet resources for proteins associated with drug therapeutic effects, adverse reactions and ADME.

Molecular basis of therapeutic approaches to gastric cancer

Multitarget inhibitors derived from crosstalk mechanism involving VEGFR2.

NOREVA: normalization and evaluation of MS-based metabolomics data

NPASS: natural product activity and species source database for natural product research, discovery and tool development

Nature's contribution to today's pharmacopeia

Neighbor communities in drug combination networks characterize synergistic effect ⬇️

Neuroprotective gases--fantasy or reality for clinical use?

Nicotine-induced neuroprotection against ischemic injury involves activation of endocannabinoid system in rats

Novel synthetic acridine derivatives as potent DNA-binding and apoptosis-inducing antitumor agents ⬇️

Overexpressed CacyBP/SIP leads to the suppression of growth in renal cell carcinoma

Pharmacological relationships and ligand discovery of G protein-coupled receptors revealed by simultaneous ligand and receptor clustering

Phthalimide conjugations for the degradation of oncogenic PI3K.

Physicochemical Profiles of the Marketed Agrochemicals and Clues for Agrochemical Lead Discovery and Screening Library Development

Polymorphisms in the vitamin D receptor gene and risk of primary biliary cirrhosis: a meta-analysis

Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway

Predicting Targeted Polypharmacology for Drug Repositioning and Multi- Target Drug Discovery ⬇️

Predicting the Enzymatic Hydrolysis Half-lives of New Chemicals Using Support Vector Regression Models Based on Stepwise Feature Elimination

Prediction of RNA-binding proteins from primary sequence by a support vector machine approach

Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines