List of works - Ziding Zhang

A new class of analgesic agents toward prostacyclin receptor inhibition: synthesis, biological studies and QSAR analysis of 1-hydroxyl-2-substituted phenyl-4,4,5,5-tetramethylimidazolines

scientific article published on 27 July 2007

A new class of anti-thrombosis hexahydropyrazino-[1',2':1,6]pyrido-[3,4-b]-indole-1,4-dions: design, synthesis, logK determination, and QSAR analysis

scientific article published on 09 June 2007

A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa

scientific article published on 16 May 2011

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features.

scientific article

An Important Role for Purifying Selection in Archaeal Genome Evolution.

scientific article published in September 2017

An improved prediction of catalytic residues in enzyme structures.

scientific article

An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins

scientific article

AtKC1 and CIPK23 Synergistically Modulate AKT1-Mediated Low-Potassium Stress Responses in Arabidopsis

scientific article published in February 2016

Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance

scientific article published on 3 July 2008

Can simple codon pair usage predict protein-protein interaction?

scientific article published on 5 March 2012

Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae

scientific article

Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors

scientific article published on 01 February 2006

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes ⬇️

scientific article published on December 23, 2011

Computational studies of ligand-receptor interactions in bitter taste receptors

scientific article published in January 2006

Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods.

scientific article published on 27 September 2017

DescFold: a web server for protein fold recognition.

scientific article

Descriptor-based protein remote homology identification

scientific article published on 4 January 2005

Evaluation of protein phosphorylation site predictors

scientific article published on 01 January 2010

Exploring the sequence-structure protein landscape in the glycosyltransferase family

scientific article published on October 2003

GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network

scientific article published on 24 July 2007

Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium

scientific article published on 30 August 2011

Genome-wide analysis of enzyme structure-function combination across three domains of life

scientific article published on 01 January 2007

How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators

scientific article

Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues

scientific article

Interaction of Positional Isomers of Quercetin Glucuronides with the Transporter ABCC2 (cMOAT, MRP2)

scientific article published on 03 May 2007

Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens

scientific article published on 24 May 2017

Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties

scientific article published on 22 April 2019

Multi-modal features-based human-herpesvirus protein–protein interaction prediction by using LightGBM

scientific article published in 2024

N-[2-(5,5-dimethyl-1,3-dioxane-2-yl)ethyl]amino acids: their synthesis, anti-inflammatory evaluation and QSAR analysis

scientific article (publication date: 2008)

Novel 1-oxyl-2-substitutedphenyl-4,4,5,5-tetramethylimidazolines: synthesis, selectively analgesic action, and QSAR analysis

scientific article

Outer membrane proteins can be simply identified using secondary structure element alignment.

scientific article

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

scientific article

Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions

scientific article

PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

scientific article published on 06 February 2020

Polysaccharide-induced order-to-order transitions in lyotropic liquid crystals

scientific article published in July 2005

Potential for dramatic improvement in sequence alignment against structures of remote homologous proteins by extracting structural information from multiple structure alignment

scientific article published on September 2003

Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach

scientific article

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

scientific article

Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles

scientific article

Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

scientific article published on 24 July 2011

Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs

scientific article published in 2011

Similarity networks of protein binding sites

scientific article published in February 2006

Solvation energy and thermal stability of hydrophilization-modified alpha-chymotrypsin

scientific article published on 01 July 1999

Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation.

scientific article published on 11 December 2013

Studies on logP, retention time and QSAR of 2-substituted phenylnitronyl nitroxides as free radical scavengers

scientific article published on 13 January 2007

TIM-Finder: a new method for identifying TIM-barrel proteins

scientific article

The AtMAP65-1 cross-bridge between microtubules is formed by one dimer

scientific article published on 15 May 2007

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity

scientific article

The hybrid protein interactome contributes to rice heterosis as epistatic effects

scientific article published on 17 November 2019

The prediction of protein-protein interaction networks in rice blast fungus

scientific article

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

scientific article published on 28 September 2021

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

scientific article published on 11 October 2021

Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework

scientific article published on 01 March 2019

Understanding the influence of AMG 510 on the structure of KRAS<sup>G12C</sup> empowered by molecular dynamics simulation

scientific article published on 24 February 2022

Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes ⬇️

scientific article published on February 20, 2013

ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.

scientific article published in September 2013

hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

scientific article

List of works by Ziding Zhang

A new class of analgesic agents toward prostacyclin receptor inhibition: synthesis, biological studies and QSAR analysis of 1-hydroxyl-2-substituted phenyl-4,4,5,5-tetramethylimidazolines

A new class of anti-thrombosis hexahydropyrazino-[1',2':1,6]pyrido-[3,4-b]-indole-1,4-dions: design, synthesis, logK determination, and QSAR analysis

A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features.

An Important Role for Purifying Selection in Archaeal Genome Evolution.

An improved prediction of catalytic residues in enzyme structures.

An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins

AtKC1 and CIPK23 Synergistically Modulate AKT1-Mediated Low-Potassium Stress Responses in Arabidopsis

Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance

Can simple codon pair usage predict protein-protein interaction?

Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae

Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes ⬇️

Computational studies of ligand-receptor interactions in bitter taste receptors

Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods.

DescFold: a web server for protein fold recognition.

Descriptor-based protein remote homology identification

Evaluation of protein phosphorylation site predictors

Exploring the sequence-structure protein landscape in the glycosyltransferase family

GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network

Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium

Genome-wide analysis of enzyme structure-function combination across three domains of life

How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators

Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues

Interaction of Positional Isomers of Quercetin Glucuronides with the Transporter ABCC2 (cMOAT, MRP2)

Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens

Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties

Multi-modal features-based human-herpesvirus protein–protein interaction prediction by using LightGBM

N-[2-(5,5-dimethyl-1,3-dioxane-2-yl)ethyl]amino acids: their synthesis, anti-inflammatory evaluation and QSAR analysis

Novel 1-oxyl-2-substitutedphenyl-4,4,5,5-tetramethylimidazolines: synthesis, selectively analgesic action, and QSAR analysis

Outer membrane proteins can be simply identified using secondary structure element alignment.

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions

PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

Polysaccharide-induced order-to-order transitions in lyotropic liquid crystals

Potential for dramatic improvement in sequence alignment against structures of remote homologous proteins by extracting structural information from multiple structure alignment

Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles

Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs

Similarity networks of protein binding sites

Solvation energy and thermal stability of hydrophilization-modified alpha-chymotrypsin

Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation.

Studies on logP, retention time and QSAR of 2-substituted phenylnitronyl nitroxides as free radical scavengers

TIM-Finder: a new method for identifying TIM-barrel proteins

The AtMAP65-1 cross-bridge between microtubules is formed by one dimer

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity

The hybrid protein interactome contributes to rice heterosis as epistatic effects

The prediction of protein-protein interaction networks in rice blast fungus

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework

Understanding the influence of AMG 510 on the structure of KRAS<sup>G12C</sup> empowered by molecular dynamics simulation

Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes ⬇️

ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.

hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties