MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J. Williams,Jeffrey J. Headd,Nigel W. Moriarty,Michael G. Prisant,Lizbeth L. Videau,Lindsay N. Deis,Vishal Verma,Daniel A. Keedy,Bradley J. Hintze,Vincent B. Chen,Swati Jain,Steven M. Lewis,W. Bryan Arendall,Jack Snoeyink,Paul D. Adams,Simon C. Lovell,Jane S. Richardson,David S. Richardson +17 more
TLDR
Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by Mol probity's unique all‐atom clashscore.Abstract:
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.read more
Citations
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Dorothee Liebschner,Pavel V. Afonine,Matthew L. Baker,Gábor Bunkóczi,Vincent B. Chen,Tristan I. Croll,Bradley J. Hintze,Li-Wei Hung,Swati Jain,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Billy K. Poon,Michael G. Prisant,Randy J. Read,Jane S. Richardson,David S. Richardson,Sammito,Oleg V. Sobolev,Duncan H. Stockwell,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Lizbeth L. Videau,Carmen J. Williams,Paul D. Adams,Paul D. Adams +26 more
TL;DR: Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
Journal ArticleDOI
Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Qihui Wang,Yanfang Zhang,Lili Wu,Sheng Niu,Sheng Niu,Chunli Song,Chunli Song,Zengyuan Zhang,Guangwen Lu,Chengpeng Qiao,Yu Hu,Yu Hu,Kwok-Yung Yuen,Qisheng Wang,Huan Zhou,Jinghua Yan,Jianxun Qi +16 more
TL;DR: The crystal structure of the C-terminal domain of SARS-CoV-2 (SARS- coV- 2-CTD) spike (S) protein in complex with human ACE2 (hACE2) is presented, which reveals a hACE2-binding mode similar overall to that observed for SARS -CoV.
Journal ArticleDOI
Accurate prediction of protein structures and interactions using a three-track neural network
Minkyung Baek,Frank DiMaio,Ivan Anishchenko,Justas Dauparas,Sergey Ovchinnikov,Gyu Rie Lee,Jue Wang,Qian Cong,Lisa N. Kinch,R. Dustin Schaeffer,Claudia Millán,Hahnbeom Park,Carson Adams,Caleb R. Glassman,Andy DeGiovanni,Jose Henrique Pereira,Andria V. Rodrigues,Alberdina A. van Dijk,Ana C. Ebrecht,Diederik J. Opperman,Theo Sagmeister,Christoph Buhlheller,Christoph Buhlheller,Tea Pavkov-Keller,Manoj K. Rathinaswamy,Udit Dalwadi,Calvin K. Yip,John E. Burke,K. Christopher Garcia,Nick V. Grishin,Paul D. Adams,Paul D. Adams,Randy J. Read,David Baker +33 more
TL;DR: In this article, a three-track network is proposed to combine information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level.
Journal ArticleDOI
Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
TL;DR: In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.
Journal ArticleDOI
A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.
Yan Wu,Yan Wu,Feiran Wang,Feiran Wang,Chenguang Shen,Weiyu Peng,Weiyu Peng,Delin Li,Cheng Zhao,Zhaohui Li,Shihua Li,Yuhai Bi,Yang Yang,Yuhuan Gong,Haixia Xiao,Zheng Fan,Shuguang Tan,Guizhen Wu,Wenjie Tan,Xuancheng Lu,Changfa Fan,Qihui Wang,Yingxia Liu,Chen Zhang,Jianxun Qi,George F. Gao,Feng Gao,Lei Liu +27 more
TL;DR: In isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities, a therapeutic study in a mouse model validated that these antibodies can reduce virus titers in infected lungs.
References
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