Using Situs for the integration of multi-resolution structures
Willy Wriggers,Willy Wriggers +1 more
TLDR
This review provides an overview of the Situs package as it exists today with an emphasis on functionality and workflows supported by version 2.5.Abstract:
Situs is a modular and widely used software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. The programs have been ported to numerous platforms in both serial and shared memory parallel architectures and can be combined in various ways for specific modeling applications. The modular design facilitates the updating of individual programs and the development of novel application workflows. This review provides an overview of the Situs package as it exists today with an emphasis on functionality and workflows supported by version 2.5.read more
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Complement is activated by IgG hexamers assembled at the cell surface.
Christoph A. Diebolder,Christoph A. Diebolder,Frank J. Beurskens,Rob N. de Jong,Roman I. Koning,Kristin Strumane,Margaret A. Lindorfer,Marleen Voorhorst,Deniz Ugurlar,Sara Rosati,Albert J. R. Heck,Jan G. J. van de Winkel,Ian A. Wilson,Abraham J. Koster,Ronald P. Taylor,Erica Ollmann Saphire,Dennis R. Burton,Dennis R. Burton,Janine Schuurman,Piet Gros,Paul W. H. I. Parren +20 more
TL;DR: This work found that specific noncovalent interactions between Fc segments of immunoglobulin G (IgG) antibodies resulted in the formation of ordered antibody hexamers after antigen binding on cells, thereby triggering the complement cascade.
Journal ArticleDOI
Cryo-em study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units
Feng Song,Ping Chen,Dapeng Sun,Mingzhu Wang,Liping Dong,Dan Liang,Rui-Ming Xu,Ping Zhu,Guohong Li +8 more
TL;DR: The 11-angstrom–resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome repeat lengths provide mechanistic insights into how nucleosomes compact into higher-order Chromatin fibers.
Journal ArticleDOI
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System
Zheng Yang,Keren Lasker,Keren Lasker,Dina Schneidman-Duhovny,Ben Webb,Conrad C. Huang,Eric F. Pettersen,Thomas D. Goddard,Elaine C. Meng,Andrej Sali,Thomas E. Ferrin,Thomas E. Ferrin +11 more
TL;DR: Several modeling tools into UCSF Chimera include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.
Journal ArticleDOI
Outcome of the First Electron Microscopy Validation Task Force Meeting
Richard Henderson,Andrej Sali,Matthew L. Baker,Bridget Carragher,Batsal Devkota,Kenneth H. Downing,Edward H. Egelman,Zukang Feng,Joachim Frank,Joachim Frank,Nikolaus Grigorieff,Wen Jiang,Steven J. Ludtke,Ohad Medalia,Pawel A. Penczek,Peter B. Rosenthal,Michael G. Rossmann,Michael F. Schmid,Gunnar F. Schröder,Alasdair C. Steven,David L. Stokes,John D. Westbrook,Willy Wriggers,Huanwang Yang,Jasmine Young,Helen M. Berman,Wah Chiu,Gerard J. Kleywegt,Catherine L. Lawson +28 more
TL;DR: This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Validation Task Force organized by the Unified Data Resource for 3DEM and aims to increase the impact of 3DEM in biology and medicine.
Journal ArticleDOI
Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody
Rui Kong,Kai Xu,Tongqing Zhou,Priyamvada Acharya,Thomas Lemmin,Kevin Liu,Gabriel Ozorowski,Gabriel Ozorowski,Cinque Soto,Justin Taft,Robert T. Bailer,Evan M. Cale,Lei Chen,Chang W. Choi,Gwo-Yu Chuang,Nicole A. Doria-Rose,Aliaksandr Druz,Ivelin S. Georgiev,Jason Gorman,Jinghe Huang,M. Gordon Joyce,Mark K. Louder,Xiaochu Ma,Krisha McKee,Sijy O'Dell,Marie Pancera,Yongping Yang,Scott C. Blanchard,Walther Mothes,Dennis R. Burton,Dennis R. Burton,Wayne C. Koff,Mark Connors,Andrew B. Ward,Andrew B. Ward,Peter D. Kwong,John R. Mascola +36 more
TL;DR: The identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry.
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