Macromolecular modeling and design in Rosetta: recent methods and frameworks-Reference-Cited by-同舟云学术

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Published:2020-06-01 Issue:7 Volume:17 Page:665-680
ISSN:1548-7091
Container-title:Nature Methods
language:en
Short-container-title:Nat Methods

Author:

Leman Julia Koehler^ORCID,Weitzner Brian D.,Lewis Steven M.,Adolf-Bryfogle Jared,Alam Nawsad,Alford Rebecca F.,Aprahamian Melanie,Baker David^ORCID,Barlow Kyle A.^ORCID,Barth Patrick,Basanta Benjamin^ORCID,Bender Brian J.,Blacklock Kristin,Bonet Jaume^ORCID,Boyken Scott E.^ORCID,Bradley Phil^ORCID,Bystroff Chris,Conway Patrick,Cooper Seth,Correia Bruno E.^ORCID,Coventry Brian,Das Rhiju^ORCID,De Jong René M.,DiMaio Frank,Dsilva Lorna,Dunbrack Roland^ORCID,Ford Alexander S.,Frenz Brandon,Fu Darwin Y.,Geniesse Caleb^ORCID,Goldschmidt Lukasz,Gowthaman Ragul^ORCID,Gray Jeffrey J.^ORCID,Gront Dominik,Guffy Sharon,Horowitz Scott,Huang Po-Ssu,Huber Thomas,Jacobs Tim M.,Jeliazkov Jeliazko R.,Johnson David K.^ORCID,Kappel Kalli^ORCID,Karanicolas John^ORCID,Khakzad Hamed^ORCID,Khar Karen R.,Khare Sagar D.,Khatib Firas^ORCID,Khramushin Alisa,King Indigo C.,Kleffner Robert,Koepnick Brian,Kortemme Tanja^ORCID,Kuenze Georg,Kuhlman Brian^ORCID,Kuroda Daisuke^ORCID,Labonte Jason W.,Lai Jason K.,Lapidoth Gideon,Leaver-Fay Andrew,Lindert Steffen,Linsky Thomas,London Nir,Lubin Joseph H.,Lyskov Sergey,Maguire Jack,Malmström Lars^ORCID,Marcos Enrique^ORCID,Marcu Orly,Marze Nicholas A.,Meiler Jens,Moretti Rocco,Mulligan Vikram Khipple,Nerli Santrupti,Norn Christoffer,Ó’Conchúir Shane,Ollikainen Noah,Ovchinnikov Sergey,Pacella Michael S.,Pan Xingjie,Park Hahnbeom,Pavlovicz Ryan E.,Pethe Manasi,Pierce Brian G.^ORCID,Pilla Kala Bharath,Raveh Barak,Renfrew P. Douglas,Burman Shourya S. Roy^ORCID,Rubenstein Aliza,Sauer Marion F.,Scheck Andreas,Schief William^ORCID,Schueler-Furman Ora,Sedan Yuval,Sevy Alexander M.^ORCID,Sgourakis Nikolaos G.,Shi Lei,Siegel Justin B.,Silva Daniel-Adriano,Smith Shannon,Song Yifan,Stein Amelie^ORCID,Szegedy Maria^ORCID,Teets Frank D.,Thyme Summer B.,Wang Ray Yu-Ruei,Watkins Andrew,Zimmerman Lior,Bonneau Richard^ORCID

Funder

Simons Foundation

Publisher

Springer Science and Business Media LLC

Subject

Cell Biology,Molecular Biology,Biochemistry,Biotechnology

Link

http://www.nature.com/articles/s41592-020-0848-2.pdf

Reference214 articles.

1. Schrödinger. Biologics design. https://www.schrodinger.com/science-articles/biologics-design (2020).

2. Chemical Computing Group. Molecular Operating Environment (MOE) | MOEsaic | PSILO. https://www.chemcomp.com/Products.htm (2020).

3. Dassault Systèmes. BIOVIA, Discovery Studio Modeling Environment, release 2017. https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/ (2016).

4. Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).

5. Vu, O., Mendenhall, J., Altarawy, D. & Meiler, J. BCL:Mol2D-a robust atom environment descriptor for QSAR modeling and lead optimization. J. Comput. Aided Mol. Des. 33, 477–486 (2019).

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