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2024

Fixed-point Encoding and Architecture Exploration for Residue Number Systems
Fixed-point Encoding and Architecture Exploration for Residue Number Systems
Bobin Deng, Bhargava Nadendla, Kun Suo, Yixin Xie, Dan Chia-Tien Lo
ACM Transactions on Architecture and Code Optimization   ·   14 Sep 2024   ·   doi:10.1145/3664923
AI-Driven Deep Learning Techniques in Protein Structure Prediction
AI-Driven Deep Learning Techniques in Protein Structure Prediction
Lingtao Chen, Qiaomu Li, Kazi Fahim Ahmad Nasif, Ying Xie, Bobin Deng, Shuteng Niu, Seyedamin Pouriyeh, Zhiyu Dai, Jiawei Chen, Chloe Yixin Xie
International Journal of Molecular Sciences   ·   01 Aug 2024   ·   doi:10.3390/ijms25158426
A Comparative Analysis of SARS-CoV-2 Variants of Concern (VOC) Spike Proteins Interacting with hACE2 Enzyme
A Comparative Analysis of SARS-CoV-2 Variants of Concern (VOC) Spike Proteins Interacting with hACE2 Enzyme
Jiawei Chen, Lingtao Chen, Heng Quan, Soongoo Lee, Kaniz Fatama Khan, Ying Xie, Qiaomu Li, Maria Valero, Zhiyu Dai, Yixin Xie
International Journal of Molecular Sciences   ·   23 Jul 2024   ·   doi:10.3390/ijms25158032
Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights
Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights
Jiawei Chen, Ravi Potlapalli, Heng Quan, Lingtao Chen, Ying Xie, Seyedamin Pouriyeh, Nazmus Sakib, Lichao Liu, Yixin Xie
BioTech   ·   16 Jan 2024   ·   doi:10.3390/biotech13010003

2023

Molecular Dynamics Simulations on Coronavirus Variants of Concern (VOC)
Molecular Dynamics Simulations on Coronavirus Variants of Concern (VOC)
Durga Narayana Varma Addepalli, Jiawei Chen, Chloe Yixin Xie
The 24th Annual Conference on Information Technology Education   ·   11 Oct 2023   ·   doi:10.1145/3585059.3611442
JAK3 Y841 Autophosphorylation Is Critical for STAT5B Activation, Kinase Domain Stability and Dimer Formation
JAK3 Y841 Autophosphorylation Is Critical for STAT5B Activation, Kinase Domain Stability and Dimer Formation
Georgialina Rodriguez, George Steven Martinez, Omar Daniel Negrete, Shengjie Sun, Wenhan Guo, Yixin Xie, Lin Li, Chuan Xiao, Jeremy Aaron Ross, Robert Arthur Kirken
International Journal of Molecular Sciences   ·   25 Jul 2023   ·   doi:10.3390/ijms241511928
Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation
Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation
Shengjie Sun, Georgialina Rodriguez, Yixin Xie, Wenhan Guo, Alan E. Lopez Hernandez, Jason E. Sanchez, Robert Arthur Kirken, Lin Li
Life   ·   10 Apr 2023   ·   doi:10.3390/life13040981

2022

DG-Labeler and DGL-MOTS dataset: Boost the autonomous driving perception
DG-Labeler and DGL-MOTS dataset: Boost the autonomous driving perception
[no author info]
arXiv   ·   07 Jun 2022   ·   eid:2-s2.0-85118005743
Computational Study on the Electrostatic Interactions between Uracil‐DNA Glycosylase (UDG) and DNA
Computational Study on the Electrostatic Interactions between Uracil‐DNA Glycosylase (UDG) and DNA
Yixin Xie, Lin Li
The FASEB Journal   ·   01 May 2022   ·   doi:10.1096/FASEBJ.2022.36.S1.0R568
Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin
Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin
Yixin Xie, Lin Li
International Journal of Molecular Sciences   ·   12 Feb 2022   ·   doi:10.3390/ijms23042035
The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2
The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2
Yixin Xie, Wenhan Guo, Alan Lopez-Hernadez, Shaolei Teng, Lin Li
Pathogens   ·   11 Feb 2022   ·   doi:10.3390/pathogens11020238

2021

Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2
Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2
Adebiyi Sobitan, Vidhyanand Mahase, Raina Rhoades, Dejaun Williams, Dongxiao Liu, Yixin Xie, Lin Li, Qiyi Tang, Shaolei Teng
Frontiers in Molecular Biosciences   ·   09 Dec 2021   ·   doi:10.3389/fmolb.2021.784303
Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA
Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA
Yixin Xie, Chitra B. Karki, Jiawei Chen, Dongfang Liu, Lin Li
Frontiers in Molecular Biosciences   ·   06 Aug 2021   ·   doi:10.3389/fmolb.2021.718587
Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2
Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2
Adebiyi Sobitan, Vidhyanand Mahase, Raina Rhoades, Dejaun Williams, Dongxiao Liu, Yixin Xie, Lin Li, Qiyi Tang, Shaolei Teng
Cold Spring Harbor Laboratory   ·   30 Jun 2021   ·   doi:10.1101/2021.06.30.450547
The Electrostatic Features of Dengue Virus Capsid Assembly
The Electrostatic Features of Dengue Virus Capsid Assembly
Alan E Lopez-Hernandez, Yixin Xie, Wenhan Guo, Lin Li
Journal of Computational Biophysics and Chemistry   ·   01 Mar 2021   ·   doi:10.1142/S2737416520420089
StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions
StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions
Yuejiao Xian, Yixin Xie, Sebastian Miki Silva, Chitra B. Karki, Weihong Qiu, Lin Li
Frontiers in Molecular Biosciences   ·   11 Jan 2021   ·   doi:10.3389/fmolb.2020.627087
Hybrid method for representing ions in implicit solvation calculations
Hybrid method for representing ions in implicit solvation calculations
Shengjie Sun, Chitra Karki, Yixin Xie, Yuejiao Xian, Wenhan Guo, Bruce Z. Gao, Lin Li
Computational and Structural Biotechnology Journal   ·   01 Jan 2021   ·   doi:10.1016/j.csbj.2021.01.020
Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2
Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2
Wenhan Guo, Yixin Xie, Alan E Lopez-Hernandez, Shengjie Sun, Lin Li
Mathematical Biosciences and Engineering   ·   01 Jan 2021   ·   doi:10.3934/MBE.2021120

2020

Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2
Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2
Yixin Xie, Chitra B. Karki, Dan Du, Haotian Li, Jun Wang, Adebiyi Sobitan, Shaolei Teng, Qiyi Tang, Lin Li
Frontiers in Molecular Biosciences   ·   09 Dec 2020   ·   doi:10.3389/fmolb.2020.591873
Revealing the Mechanism of SARS-CoV-2 Spike Protein Binding With ACE2
Revealing the Mechanism of SARS-CoV-2 Spike Protein Binding With ACE2
Yixin Xie, Dan Du, Chitra B. Karki, Wenhan Guo, Alan E Lopez-Hernandez, Shengjie Sun, Brenda Y Juarez, Haotian Li, Jun Wang, Lin Li
Computing in Science & Engineering   ·   01 Nov 2020   ·   doi:10.1109/MCSE.2020.3015511
Computational analysis of hereditary spastic paraplegia mutations in the kinesin motor domains of KIF1A and KIF5A
Computational analysis of hereditary spastic paraplegia mutations in the kinesin motor domains of KIF1A and KIF5A
Vidhyanand Mahase, Adebiyi Sobitan, Christina Johnson, Farion Cooper, Yixin Xie, Lin Li, Shaolei Teng
Journal of Theoretical and Computational Chemistry   ·   05 Aug 2020   ·   doi:10.1142/S0219633620410035
A computational model of ESAT-6 complex in membrane
A computational model of ESAT-6 complex in membrane
Chitra Karki, Yuejiao Xian, Yixin Xie, Shengjie Sun, Alan E Lopez-Hernandez, Brenda Juarez, Jun Wang, Jianjun Sun, Lin Li
Journal of Theoretical and Computational Chemistry   ·   17 Mar 2020   ·   doi:10.1142/S0219633620400027

2019

Using computational approaches to study dengue virus capsid assembly
Using computational approaches to study dengue virus capsid assembly
Gicela G Saucedo Salas, Alan E Lopez Hernandez, Jiadi He, Chitra Karki, Yixin Xie, Shengjie Sun, Yuejiao Xian, Lin Li
Computational and Mathematical Biophysics   ·   01 Jan 2019   ·   doi:10.1515/cmb-2019-0005