Haipeng Gong

发表

Cancer-cell-derived fumarate suppresses the anti-tumor capacity of CD8+ T cells in the tumor microenvironment.

H. Gong, P. Jiang, Xinxiang Zhang, 2023, Cell metabolism.

A deep learning framework for modeling structural features of RNA-binding protein targets

Jianyang Zeng, Sai Zhang, Jingtian Zhou, 2015, Nucleic acids research.

RBRIdent: An algorithm for improved identification of RNA‐binding residues in proteins from primary sequences

Dapeng Xiong, Jianyang Zeng, Haipeng Gong, 2015, Proteins.

Coupling between ATP hydrolysis and protein conformational change in maltose transporter

H. Liu, H. Gong, Haifeng Chen, 2017, Proteins.

Protein design via deep learning

K. Nakai, H. Gong, Wenze Ding, 2022, Briefings Bioinform..

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction

Tong Wang, Yaoqi Zhou, Yuedong Yang, 2016, Bioinform..

SAMF: a self-adaptive protein modeling framework

Haipeng Gong, Wenze Ding, Tie-Yan Liu, 2021, Bioinform..

Improving the orientation‐dependent statistical potential using a reference state

Jianyang Zeng, Haipeng Gong, Yufeng Liu, 2014, Proteins.

A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis

H. Gong, Xinquan Wang, Xinqi Gong, 2013, Cell Research.

A novel implicit solvent model for simulating the molecular dynamics of RNA.

H. Gong, K. Freed, T. Sosnick, 2013, Biophysical journal.

Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins.

H. Gong, K. Freed, Haipeng Gong, 2010, Biophysical journal.

Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model

Haipeng Gong, Karl F. Freed, Glen M. Hocky, 2008, Proceedings of the National Academy of Sciences.

Identifying a Feasible Transition Pathway between Two Conformational States for a Protein.

H. Gong, Yao Li, Haipeng Gong, 2022, Journal of chemical theory and computation.

Exploring the Regulatory Function of the N‐terminal Domain of SARS‐CoV‐2 Spike Protein through Molecular Dynamics Simulation

Tie-Yan Liu, H. Gong, Tong Wang, 2021, Advanced theory and simulations.

Theoretical and simulation studies on voltage-gated sodium channels

H. Gong, Yang Li, Haipeng Gong, 2015, Protein & Cell.

Predicting the Real‐Valued Inter‐Residue Distances for Proteins

Haipeng Gong, Wenze Ding, H. Gong, 2020, Advanced science.

AmoebaContact and GDFold: a new pipeline for rapid prediction of protein structures

Haipeng Gong, Wenzhi Mao, Wenze Ding, 2019, 1905.11640.

Data construction for phosphorylation site prediction

Jun Wu, Zengyou He, Xiaoqing Liu, 2014, Briefings Bioinform..

Increasing βB1-crystallin sensitivity to proteolysis caused by the congenital cataract-microcornea syndrome mutation S129R.

H. Gong, Huihui Liu, Yong-Bin Yan, 2013, Biochimica et biophysica acta.

Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy

Yunxin Xu, Di Liu, Haipeng Gong, 2023, bioRxiv.

Structural and Dynamic Insights into the Mechanism of Allosteric Signal Transmission in ERK2-Mediated MKP3 Activation.

Haipeng Gong, Zhi-Xin Wang, H. Gong, 2017, Biochemistry.

Large-scale molecular dynamics simulation of coupled dynamics of flow and glycocalyx: towards understanding atomic events on an endothelial cell surface

H. Gong, Y. Ventikos, K. Luo, 2017, Journal of The Royal Society Interface.

Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field.

H. Gong, Rui-Ning Sun, Haipeng Gong, 2017, The journal of physical chemistry letters.

Structural bioinformatics LRFragLib : an effective algorithm to identify fragments for de novo protein structure prediction

Yaoqi Zhou, Yuedong Yang, H. Gong, 2017 .

Predicting the helix‐helix interactions from correlated residue mutations

H. Gong, Wenzhi Mao, Dapeng Xiong, 2017, Proteins.

A deep learning framework for improving long‐range residue‐residue contact prediction using a hierarchical strategy

Dapeng Xiong, Jianyang Zeng, Haipeng Gong, 2017, Bioinform..

Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel.

H. Gong, Huihui Liu, Yang Li, 2017, Biochimica et biophysica acta. Biomembranes.

Impairment on the lateral mobility induced by structural changes underlies the functional deficiency of the lupus-associated polymorphism FcγRIIB-T232

Zhibin Hu, H. Gong, T. Meckel, 2016, The Journal of experimental medicine.

Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation.

H. Gong, Huihui Liu, M. Ke, 2013, Biophysical journal.

The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation.

N. Yan, Huihui Liu, Mengdie Xia, 2013, Biophysical journal.

Analysis of the selectivity filter of the voltage-gated sodium channel NavRh

D. Clapham, H. Gong, Jianping Wu, 2012, Cell Research.

Mining Conditional Phosphorylation Motifs

Jun Wu, Zengyou He, Shengchun Deng, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models

H. Gong, Xiaolei Zhu, Yanhua Qiao, 2021, Bioinform..

Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly

Yang Shen, Haipeng Gong, George D Rose, 2007, Protein science : a publication of the Protein Society.

Secondary structure determines protein topology

G. Rose, H. Gong, P. Fleming, 2006, Protein science : a publication of the Protein Society.

DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening

Jianyang Zeng, Yue Zhu, Tian Xia, 2019, Genom. Proteom. Bioinform..

Frontier expansion sampling: a method to accelerate conformational search by identifying novel seed structures for restart.

Juanrong Zhang, Haipeng Gong, H. Gong, 2020, Journal of chemical theory and computation.

Counting peptide‐water hydrogen bonds in unfolded proteins

G. Rose, H. Gong, Lauren L. Porter, 2011, Protein science : a publication of the Protein Society.

A PIP2-derived amplification loop fuels the sustained initiation of B cell activation

Hai Qi, H. Gong, Lei Liu, 2017, Science Immunology.

Using the unfolded state as the reference state improves the performance of statistical potentials.

Haipeng Gong, Yufeng Liu, H. Gong, 2012, Biophysical journal.

Mechanism of actions of Oncocin, a proline-rich antimicrobial peptide, in early elongation revealed by single-molecule FRET

Wenjuan Wang, Chunlai Chen, Q. Xi, 2017, Protein & Cell.

RDb2C2: an improved method to identify the residue-residue pairing in β strands

Haipeng Gong, Di Shao, Wenzhi Mao, 2020, BMC Bioinformatics.

Identification of residue pairing in interacting β-strands from a predicted residue contact map

Tong Wang, Wenxuan Zhang, Haipeng Gong, 2017, BMC Bioinformatics.

Local secondary structure content predicts folding rates for simple, two-state proteins.

Haipeng Gong, Rajgopal Srinivasan, George D Rose, 2003, Journal of molecular biology.

ProteinLasso: A Lasso regression approach to protein inference problem in shotgun proteomics

Zengyou He, Can Yang, Ting Huang, 2013, Comput. Biol. Chem..

EvoAI enables extreme compression and reconstruction of the protein sequence space

Christopher A. Voigt, David R. Liu, Haipeng Gong, 2024, Research square.

Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding

E. Shakhnovich, H. Gong, Tong Wang, 2019, 1906.05785.

Structure of the human voltage-gated sodium channel Nav1.4 in complex with β1

H. Gong, Qiang Zhou, N. Yan, 2018, Science.

Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data

Jianyang Zeng, Sai Zhang, Haipeng Gong, 2015, RECOMB.

Structure of a fucose transporter in an outward-open conformation

H. Gong, N. Yan, Yufeng Liu, 2010, Nature.

Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model

G. Rose, H. Gong, Haipeng Gong, 2008, Proceedings of the National Academy of Sciences.