Visualization of macromolecular structures

被引:0
作者
O'Donoghue, Sean I. [1 ]
Goodsell, David S. [2 ]
Frangakis, Achilleas S. [3 ]
Jossinet, Fabrice [4 ]
Laskowski, Roman A. [5 ]
Nilges, Michael [6 ]
Saibil, Helen R. [7 ]
Schafferhans, Andrea [1 ]
Wade, Rebecca C. [8 ]
Westhof, Eric [4 ]
Olson, Arthur J. [2 ]
机构
[1] European Mol Biol Lab, Heidelberg, Germany
[2] Scripps Res Inst, La Jolla, CA 92037 USA
[3] Goethe Univ Frankfurt, Frankfurt, Germany
[4] Univ Strasbourg, CNRS, Inst Biol Mol & Cellulaire, Strasbourg, France
[5] European Bioinformat Inst, Cambridge, England
[6] Inst Pasteur, Paris, France
[7] Univ London Birkbeck Coll, Inst Struct & Mol Biol, London WC1E 7HX, England
[8] HITS, Heidelberg, Germany
关键词
3-DIMENSIONAL STRUCTURES; LIGAND-BINDING; MOLECULAR-DYNAMICS; CRYSTAL-STRUCTURE; FUNCTIONAL SITES; SWISS-MODEL; IMAGE DATA; PROTEIN; DATABASE; DESIGN;
D O I
10.1038/NMETH.1427
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Structural biology is rapidly accumulating a wealth of detailed information about protein function, binding sites, RNA, large assemblies and molecular motions. These data are increasingly of interest to a broader community of life scientists, not just structural experts. Visualization is a primary means for accessing and using these data, yet visualization is also a stumbling block that prevents many life scientists from benefiting from three-dimensional structural data. In this review, we focus on key biological questions where visualizing three-dimensional structures can provide insight and describe available methods and tools.
引用
收藏
页码:S42 / S55
页数:14
相关论文
共 50 条
  • [31] Biological function derived from predicted structures in CASP11
    Huwe, Peter J.
    Xu, Qifang
    Shapovalov, Maxim V.
    Modi, Vivek
    Andrake, Mark D.
    Dunbrack, Roland L., Jr.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016, 84 : 370 - 391
  • [32] DSSR-enhanced visualization of nucleic acid structures in Jmol
    Hanson, Robert M.
    Lu, Xiang-Jun
    NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) : W528 - W533
  • [33] Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB
    Hendrickx, Pieter M. S.
    Gutmanas, Aleksandras
    Kleywegt, Gerard J.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2013, 81 (04) : 583 - 591
  • [34] Detection and visualization of anomalous structures in molecular dynamics simulation data
    Mehta, S
    Hazzard, K
    Machiraju, R
    Parthasarathy, S
    Wilkins, J
    IEEE VISUALIZATION 2004, PROCEEEDINGS, 2004, : 465 - 472
  • [35] Topological analysis and interactive visualization of biological networks and protein structures
    Doncheva, Nadezhda T.
    Assenov, Yassen
    Domingues, Francisco S.
    Albrecht, Mario
    NATURE PROTOCOLS, 2012, 7 (04) : 670 - 685
  • [36] Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography
    Bruno, Andrew E.
    Ruby, Amanda M.
    Luft, Joseph R.
    Grant, Thomas D.
    Seetharaman, Jayaraman
    Montelione, Gaetano T.
    Hunt, John F.
    Snell, Edward H.
    PLOS ONE, 2014, 9 (06):
  • [37] OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
    Young, Jasmine Y.
    Westbrook, John D.
    Feng, Zukang
    Sala, Raul
    Peisach, Ezra
    Oldfield, Thomas J.
    Sen, Sanchayita
    Gutmanas, Aleksandras
    Armstrong, David R.
    Berrisford, John M.
    Chen, Li
    Chen, Minyu
    Di Costanzo, Luigi
    Dimitropoulos, Dimitris
    Gao, Guanghua
    Ghosh, Sutapa
    Gore, Swanand
    Guranovic, Vladimir
    Hendrickx, Pieter M. S.
    Hudson, Brian P.
    Igarashi, Reiko
    Ikegawa, Yasuyo
    Kobayashi, Naohiro
    Lawson, Catherine L.
    Liang, Yuhe
    Mading, Steve
    Mak, Lora
    Mir, M. Saqib
    Mukhopadhyay, Abhik
    Patwardhan, Ardan
    Persikova, Irina
    Rinaldi, Luana
    Sanz-Garcia, Eduardo
    Sekharan, Monica R.
    Shao, Chenghua
    Swaminathan, G. Jawahar
    Tan, Lihua
    Ulrich, Eldon L.
    van Ginkel, Glen
    Yamashita, Reiko
    Yang, Huanwang
    Zhuravleva, Marina A.
    Quesada, Martha
    Kleywegt, Gerard J.
    Berman, Helen M.
    Markley, John L.
    Nakamura, Haruki
    Velankar, Sameer
    Burley, Stephen K.
    STRUCTURE, 2017, 25 (03) : 536 - 545
  • [38] A history of experimental phasing in macromolecular crystallography
    Isaacs, Neil
    ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2016, 72 : 293 - 295
  • [39] G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures
    Solomon, Oz
    Kunik, Vered
    Simon, Amos
    Kol, Nitzan
    Barel, Ortal
    Lev, Atar
    Amariglio, Ninette
    Somech, Raz
    Rechavi, Gidi
    Eyal, Eran
    BMC GENOMICS, 2016, 17
  • [40] Glucose 6-phosphate and alcohol dehydrogenase activities are components of dynamic macromolecular depots structures
    Tramonti, Angela
    Saliola, Michele
    BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2015, 1850 (06): : 1120 - 1130