List of works - Feng Zhu

A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies

scientific article published on 12 June 2019

A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks

scientific article published on 19 August 2016

A resource for facilitating the development of tools in the education and implementation of genomics-informed personalized medicine

scientific article published on 20 February 2014

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

scientific article published on 15 January 2019

Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection

scientific article published on 01 January 2020

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

scientific article published in 2024

Assessing the Effectiveness of Direct Data Merging Strategy in Long-Term and Large-Scale Pharmacometabonomics

scientific article published on 20 February 2019

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

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

scholarly article by Fu Chen published in September 2018

Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions

scientific article published on 27 August 2019

Biomarker Discovery for Immunotherapy of Pituitary Adenomas: Enhanced Robustness and Prediction Ability by Modern Computational Tools ⬇️

journal article from 'International Journal of Molecular Sciences' published in 2019

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

scientific article published on 07 June 2018

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

scientific article published on 30 December 2017

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

scientific article published on 23 January 2019

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

scientific article published on 03 October 2015

Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation.

scientific article published on 3 November 2017

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks.

scientific article published on 28 July 2016

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

scientific article published on 31 October 2018

Computational Advances in the Label-free Quantification of Cancer Proteomics Data

scientific article published on 01 January 2018

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

scientific article published on 01 November 2018

Computational design and modeling of nanobodies toward SARS-CoV-2 receptor binding domain

scientific article published on 13 May 2021

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

Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data

scientific article published on 03 June 2019

CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses

scientific article published in 2024

Databases for the Targeted COVID-19 Therapeutics

scientific article published on 26 August 2020

Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target

scientific article published on 31 October 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 Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening

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

Evidence for possible role of toll-like receptor 3 mediating virus-induced progression of pituitary adenomas.

scientific article published on 15 February 2016

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

Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study

scientific article (publication date: 27 May 2016)

Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data

scientific article published on 24 April 2019

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

scientific article published on 01 July 2019

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

scientific article

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

scientific article published on 26 February 2019

How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study.

scientific article published on 22 August 2017

Identification of dual active agents targeting 5-HT1A and SERT by combinatorial virtual screening methods.

scientific article published on August 2015

Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis.

scientific article published on 14 August 2018

Identification of the gene signature reflecting schizophrenia's etiology by constructing artificial intelligence-based method of enhanced reproducibility

scientific article published on 27 July 2019

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

Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease

scientific article published on 21 April 2021

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK.

scientific article published on 31 January 2018

Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study

scientific article published on 05 June 2019

LncRNA functional annotation with improved false discovery rate achieved by disease associations

scientific article published on 16 December 2021

Mechanisms of drug combinations: interaction and network perspectives

scientific article published on 01 February 2009

Metformin inhibits proliferation and growth hormone secretion of GH3 pituitary adenoma cells.

scientific article

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics

scientific article published in 2024

NOREVA: normalization and evaluation of MS-based metabolomics data

scientific article

Nature's contribution to today's pharmacopeia.

scientific article published in October 2014

PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks

scientific article published on 11 October 2016

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

scientific article

Prediction of GluN2B-CT/DAPK1 Interaction by Protein⁻Peptide Docking and Molecular Dynamics Simulation

Prediction of factor Xa inhibitors by machine learning methods.

scientific article

Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H

scientific article published in 2018

Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning

scientific article published on 02 August 2019

Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters

article

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

scientific article published on 01 January 2019

Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools.

scientific article published on 30 May 2015

Reliability of Docking-Based Virtual Screening for GPCR Ligands with Homology Modeled Structures: A Case Study of the Angiotensin II Type I Receptor

scientific article published on 17 October 2018

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

SCP2-mediated cholesterol membrane trafficking promotes the growth of pituitary adenomas via Hedgehog signaling activation

scientific article published on 13 September 2019

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

scientific article

Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

scientific article published on 16 May 2019

Structure-Based Drug Design and Identification of H2O-Soluble and Low Toxic Hexacyclic Camptothecin Derivatives with Improved Efficacy in Cancer and Lethal Inflammation Models in Vivo

article

Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness.

scientific article published on 7 March 2007

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

scientific article published on 16 February 2023

The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective

scientific article

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

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

VARIDT 1.0: variability of drug transporter database

scientific article published on 01 January 2020

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 Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs' Species Origin, Druglikeness, Target and Pathway

scientific article published on 01 January 2019

What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical, and systems profiles of successful targets.

scientific article

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

scientific article published on 01 May 2019

List of works by Feng Zhu

A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies

A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks

A resource for facilitating the development of tools in the education and implementation of genomics-informed personalized medicine

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding

Assessing the Effectiveness of Direct Data Merging Strategy in Long-Term and Large-Scale Pharmacometabonomics

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

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions

Biomarker Discovery for Immunotherapy of Pituitary Adenomas: Enhanced Robustness and Prediction Ability by Modern Computational Tools ⬇️

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

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

Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation.

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks.

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

Computational Advances in the Label-free Quantification of Cancer Proteomics Data

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

Computational design and modeling of nanobodies toward SARS-CoV-2 receptor binding domain

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

Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data

CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses

Databases for the Targeted COVID-19 Therapeutics

Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target

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 Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening

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

Evidence for possible role of toll-like receptor 3 mediating virus-induced progression of pituitary adenomas.

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

Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study

Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

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

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study.

Identification of dual active agents targeting 5-HT1A and SERT by combinatorial virtual screening methods.

Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis.

Identification of the gene signature reflecting schizophrenia's etiology by constructing artificial intelligence-based method of enhanced reproducibility

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

Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK.

Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study

LncRNA functional annotation with improved false discovery rate achieved by disease associations

Mechanisms of drug combinations: interaction and network perspectives

Metformin inhibits proliferation and growth hormone secretion of GH3 pituitary adenoma cells.

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics

NOREVA: normalization and evaluation of MS-based metabolomics data

Nature's contribution to today's pharmacopeia.

PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

Prediction of GluN2B-CT/DAPK1 Interaction by Protein⁻Peptide Docking and Molecular Dynamics Simulation

Prediction of factor Xa inhibitors by machine learning methods.

Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H

Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning

Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools.

Reliability of Docking-Based Virtual Screening for GPCR Ligands with Homology Modeled Structures: A Case Study of the Angiotensin II Type I Receptor

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

SCP2-mediated cholesterol membrane trafficking promotes the growth of pituitary adenomas via Hedgehog signaling activation

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

Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

Structure-Based Drug Design and Identification of H2O-Soluble and Low Toxic Hexacyclic Camptothecin Derivatives with Improved Efficacy in Cancer and Lethal Inflammation Models in Vivo

Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness.

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective

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

Therapeutic target database update 2014: a resource for targeted therapeutics

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

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

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

VARIDT 1.0: variability of drug transporter database

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.

What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs' Species Origin, Druglikeness, Target and Pathway

What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical, and systems profiles of successful targets.