Publications

This is Shikai's publications by categories in reversed chronological order. * denotes equal contribution

2023

  1. NAR
    Structural basis of DNA polymerase θmediated DNA end joining
    Chuxuan Li, Hanwen Zhu,  Shikai Jin, Leora M Maksoud, Nikhil Jain, Ji Sun, and Yang Gao
    Nucleic Acids Research 2023
  2. PNAS
    The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor
    Xun Chen*,  Shikai Jin*, Mingchen Chen*, Carlos Bueno, and Peter G Wolynes
    Proceedings of the National Academy of Sciences 2023
  3. IUCrJ
    A deep learning solution for crystallographic structure determination
    Tom Pan*,  Shikai Jin*, Mitchell D Miller*, Anastasios Kyrillidis, and George N Phillips
    IUCrJ 2023

2022

  1. JBP
    Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model
    Xun Chen, Wei Lu, Min-Yeh Tsai,  Shikai Jin, and Peter G Wolynes
    Journal of Biological Physics 2022
  2. PNAS
    Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA
    Shikai Jin, Carlos Bueno, Wei Lu, Qian Wang, Mingchen Chen, Xun Chen, Peter G Wolynes, and Yang Gao
    Proceedings of the National Academy of Sciences 2022
  3. Nat Comm
    Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation
    Yuda Chen,  Shikai Jin, Mengxi Zhang, Yu Hu, Kuan-Lin Wu, Anna Chung, Shichao Wang, Zeru Tian, Yixian Wang, Peter G Wolynes, and others
    Nature Communications 2022

2021

  1. PLoS Comp Bio
    OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
    Wei Lu, Carlos Bueno, Nicholas P Schafer, Joshua Moller,  Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J Pablo, and others
    PLoS computational biology 2021

2020

  1. NAR
    AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes
    Shikai Jin, Vinicius G Contessoto, Mingchen Chen, Nicholas P Schafer, Wei Lu, Xun Chen, Carlos Bueno, Arya Hajitaheri, Brian J Sirovetz, Aram Davtyan, and others
    Nucleic Acids Research 2020
  2. JCTC
    Protein structure prediction in CASP13 using AWSEM-Suite
    Shikai Jin*, Mingchen Chen*, Xun Chen*, Carlos Bueno, Wei Lu, Nicholas P Schafer, Xingcheng Lin, José N Onuchic, and Peter G Wolynes
    Journal of Chemical Theory and Computation 2020
  3. JPCB
    Protein structure refinement guided by atomic packing frustration analysis
    Mingchen Chen*, Xun Chen*,  Shikai Jin, Wei Lu, Xingcheng Lin, and Peter G Wolynes
    The Journal of Physical Chemistry B 2020
  4. IUCrJ
    Molecular-replacement phasing using predicted protein structures from AWSEM-Suite
    Shikai Jin, Mitchell D Miller, Mingchen Chen, Nicholas P Schafer, Xingcheng Lin, Xun Chen, George N Phillips, and Peter G Wolynes
    IUCrJ 2020

2019

  1. PNAS
    Forging tools for refining predicted protein structures
    Xingcheng Lin, Nicholas P Schafer, Wei Lu,  Shikai Jin, Xun Chen, Mingchen Chen, José N Onuchic, and Peter G Wolynes
    Proceedings of the National Academy of Sciences 2019