Damped Dynamics as a Validation Platform for the Flexible Refinement of Atomic Models Against Cryo-EM Maps

被引:0
|
作者
Wriggers, Willy R. [1 ]
Galkin, Vitold E. [2 ]
Hunter, Wade A. [1 ]
Kovacs, Julio A. [1 ]
机构
[1] Old Dominion Univ, Dept Mech & Aerosp Engn, Norfolk, VA USA
[2] Eastern Virginia Med Sch, Dept Physiol Sci, Norfolk, VA 23501 USA
关键词
D O I
暂无
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
1426-Pos
引用
收藏
页码:292A / 292A
页数:1
相关论文
共 50 条
  • [41] Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation
    Alshammari, Maytha
    He, Jing
    Wriggers, Willy
    BIOINFORMATICS ADVANCES, 2025, 5 (01):
  • [42] Real-space refinement of ribosome crystal structure into the cryo-EM maps using YAMMP.
    Devkota, Batsal
    Li, Wen
    Frank, Joachim
    Harvey, Stephen C.
    BIOPHYSICAL JOURNAL, 2007, : 564A - 564A
  • [43] Using Combined Features to Analyze Atomic Structures Derived from Cryo-EM Density Maps
    Chen, Lin
    He, Jing
    ACM-BCB'18: PROCEEDINGS OF THE 2018 ACM INTERNATIONAL CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY, AND HEALTH INFORMATICS, 2018, : 651 - 655
  • [44] Extraction of protein dynamics information from cryo-EM maps using deep learning
    Matsumoto, Shigeyuki
    Ishida, Shoichi
    Araki, Mitsugu
    Kato, Takayuki
    Terayama, Kei
    Okuno, Yasushi
    NATURE MACHINE INTELLIGENCE, 2021, 3 (02) : 153 - 160
  • [45] Extraction of protein dynamics information from cryo-EM maps using deep learning
    Shigeyuki Matsumoto
    Shoichi Ishida
    Mitsugu Araki
    Takayuki Kato
    Kei Terayama
    Yasushi Okuno
    Nature Machine Intelligence, 2021, 3 : 153 - 160
  • [46] Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser
    Agarwal, Ishaant
    Kaczmar-Michalska, Joanna
    Norrelykke, Simon F.
    Rzepiela, Andrzej J.
    IUCRJ, 2024, 11 : 821 - 830
  • [47] CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps
    Mulvaney, Thomas
    Kretsch, Rachael C.
    Elliott, Luc
    Beton, Joseph G.
    Kryshtafovych, Andriy
    Rigden, Daniel J.
    Das, Rhiju
    Topf, Maya
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023, 91 (12) : 1935 - 1951
  • [48] Balancing Stereochemistry and Goodness-of-Fit for Automated Simulation-Based Refinement into Cryo-EM Maps
    Axelsson, Linnea S.
    Rovsnik, Urska
    Blau, Christian
    Lycksell, Marie
    Lim, Victoria
    Howard, Rebecca J.
    Lindahl, Erik R.
    BIOPHYSICAL JOURNAL, 2021, 120 (03) : 173A - 173A
  • [49] Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
    Read, Randy J.
    Millan, Claudia
    McCoy, Airlie J.
    Terwilliger, Thomas C.
    ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2023, 79 : 271 - 280
  • [50] Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution
    Kulik, Marta
    Mori, Takaharu
    Sugita, Yuji
    FRONTIERS IN MOLECULAR BIOSCIENCES, 2021, 8