List of works - Peng Tao

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes

scientific article published on 21 May 2012

A toolkit to assist ONIOM calculations.

scientific article

Ab initio classical trajectory study of the fragmentation of C3H4 dications on the singlet and triplet surfaces.

scientific article

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

scientific article published on 19 February 2019

An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps

scientific article published on 12 September 2018

Chemiluminescent Probes for Imaging H2S in Living Animals

scientific article published on March 2015

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily

scientific article

Common basis for the mechanism of metallo and non-metallo KDO8P synthases

scientific article published on 19 August 2010

Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

scientific article published on 27 September 2012

Computational Modeling of Human Paraoxonase 1: Preparation of Protein Models, Binding Studies, and Mechanistic Insights.

scientific article published on April 2010

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

scientific article published on 15 August 2014

DFT studies of the ring-opening mechanism of SB-3CT, a potent inhibitor of matrix metalloproteinase 2.

scientific article

Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods

scientific article published on 04 August 2020

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

scientific article published on 26 July 2021

Direct Measurement of Charge Regulation in Metalloprotein Electron Transfer.

scientific article published on 16 February 2018

Directed kinetic transition network model

scientific article published on 01 October 2019

Dynamics Sampling in Transition Pathway Space.

scientific article published on 30 November 2017

Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis

scientific article

Exploring free energy profile of petroleum thermal cracking mechanisms

scientific article published on 19 December 2019

Graph-learning guided mechanistic insights into imipenem hydrolysis in GES carbapenemases

scientific article published in 2022

Identifying key residues for protein allostery through rigid residue scan

scientific article

Insights into Key Interactions between Vancomycin and Bacterial Cell Wall Structures

scientific article published on 4 January 2018

Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

scientific article (publication date: 7 October 2012)

Matrix metalloproteinase 2 (MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT.

scientific article

Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.

scientific article

Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways

scientific article published in 2022

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

scientific article published on 30 October 2014

Photomodulated chiral induction in helical azobenzene oligomers

scientific article published on 09 April 2008

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps

scientific article published on 21 October 2019

Protein ligand docking based on empirical method for binding affinity estimation

scientific article published on 01 May 2001

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue ⬇️

scientific article published on November 9, 2010

REDAN: relative entropy-based dynamical allosteric network model

scientific article published on 11 November 2018

Recognition of protein allosteric states and residues: Machine learning approaches

scientific article

Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations

scientific article

Right- and Left-Handed Helices, What is in between? Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/m-(phenylazo)azobenzene Oligomers

scientific article published on 18 September 2012

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

scientific article

Synthesis ofl-Daunosamine andl-Ristosamine Glycosides via Photoinduced Aziridination. Conversion to Thioglycosides for Use in Glycosylation Reactions

scientific article published on 01 October 2006

The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem

scientific article published on 31 May 2016

The energy landscape of 3-deoxy-D-manno-octulosonate 8-phosphate synthase

scientific article published in December 2009

List of works by Peng Tao

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes

A toolkit to assist ONIOM calculations.

Ab initio classical trajectory study of the fragmentation of C3H4 dications on the singlet and triplet surfaces.

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps

Chemiluminescent Probes for Imaging H2S in Living Animals

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily

Common basis for the mechanism of metallo and non-metallo KDO8P synthases

Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

Computational Modeling of Human Paraoxonase 1: Preparation of Protein Models, Binding Studies, and Mechanistic Insights.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

DFT studies of the ring-opening mechanism of SB-3CT, a potent inhibitor of matrix metalloproteinase 2.

Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

Direct Measurement of Charge Regulation in Metalloprotein Electron Transfer.

Directed kinetic transition network model

Dynamics Sampling in Transition Pathway Space.

Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis

Exploring free energy profile of petroleum thermal cracking mechanisms

Graph-learning guided mechanistic insights into imipenem hydrolysis in GES carbapenemases

Identifying key residues for protein allostery through rigid residue scan

Insights into Key Interactions between Vancomycin and Bacterial Cell Wall Structures

Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

Matrix metalloproteinase 2 (MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT.

Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.

Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

Photomodulated chiral induction in helical azobenzene oligomers

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps

Protein ligand docking based on empirical method for binding affinity estimation

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue ⬇️

REDAN: relative entropy-based dynamical allosteric network model

Recognition of protein allosteric states and residues: Machine learning approaches

Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations

Right- and Left-Handed Helices, What is in between? Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/m-(phenylazo)azobenzene Oligomers

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

Synthesis ofl-Daunosamine andl-Ristosamine Glycosides via Photoinduced Aziridination. Conversion to Thioglycosides for Use in Glycosylation Reactions

The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem

The energy landscape of 3-deoxy-D-manno-octulosonate 8-phosphate synthase