PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
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TLDR
The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.Abstract:
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.read more
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Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
Silvana Konermann,Peter Lotfy,Nicholas J. Brideau,Jennifer Oki,Maxim N. Shokhirev,Patrick D. Hsu +5 more
TL;DR: This work identifies an uncharacterized family of RNA-guided, RNA-targeting CRISPR systems that is classified as type VI-D, and presents CasRx as a programmable RNA-binding module for efficient targeting of cellular RNA, enabling a general platform for transcriptome engineering and future therapeutic development.
Journal Article
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX autosol wizard
TL;DR: In this paper, a Bayesian approach to estimating map quality is developed and used in the PHENIX AutoSol wizard to make decisions during automated structure solution, and the skewness of electron density is found to be the best indicator of actual map quality.
Journal ArticleDOI
Crystal structure determination and refinement via SIR2014
Maria Cristina Burla,Rocco Caliandro,Benedetta Carrozzini,Giovanni Luca Cascarano,Corrado Cuocci,Carmelo Giacovazzo,Mariarosaria Mallamo,Annamaria Mazzone,Giampiero Polidori +8 more
TL;DR: SIR2014 as discussed by the authors is the latest program of the SIR suite for crystal structure solution of small, medium and large structures, which contains tools for crystal refinement and for the study of three-dimensional electron density maps via suitable viewers.
Journal ArticleDOI
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies.
Christopher O. Barnes,Anthony P. West,Kathryn E. Huey-Tubman,Magnus A.G. Hoffmann,Naima G. Sharaf,Pauline R. Hoffman,Nicholas Koranda,Harry B. Gristick,Christian Gaebler,Frauke Muecksch,Julio C. C. Lorenzi,Shlomo Finkin,Thomas Hagglof,Arlene Hurley,Katrina G. Millard,Yiska Weisblum,Fabian Schmidt,Theodora Hatziioannou,Paul D. Bieniasz,Paul D. Bieniasz,Marina Caskey,Davide F. Robbiani,Michel C. Nussenzweig,Michel C. Nussenzweig,Pamela J. Bjorkman +24 more
TL;DR: Overall, the studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/Vh3-66 and similarity to a SARS- coV VH 3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
Journal ArticleDOI
Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors.
TL;DR: This structure illuminates the assembly of the coronavirus core RNA-synthesis machinery, provides key insights into nsp12 polymerase catalysis and fidelity and acts as a template for the design of novel antiviral therapeutics.
References
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