Literature DB >> 21926992

Crystal structure of a monomeric retroviral protease solved by protein folding game players.

Firas Khatib1, Frank DiMaio, Seth Cooper, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, Iva Pichova, James Thompson, Zoran Popović, Mariusz Jaskolski, David Baker.   

Abstract

Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to produce accurate models of the protein. Remarkably, Foldit players were able to generate models of sufficient quality for successful molecular replacement and subsequent structure determination. The refined structure provides new insights for the design of antiretroviral drugs.

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Year:  2011        PMID: 21926992      PMCID: PMC3705907          DOI: 10.1038/nsmb.2119

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN: 1545-9985            Impact factor:   15.369


  11 in total

Review 1.  Structural and biochemical studies of retroviral proteases.

Authors:  A Wlodawer; A Gustchina
Journal:  Biochim Biophys Acta       Date:  2000-03-07

2.  Three-dimensional structure of a monomeric form of a retroviral protease.

Authors:  Václav Veverka; Helena Bauerová; Ales Zábranský; Jan Lang; Tomás Ruml; Iva Pichová; Richard Hrabal
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

3.  Protein structure prediction using Rosetta.

Authors:  Carol A Rohl; Charlie E M Strauss; Kira M S Misura; David Baker
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

4.  Assessment of protein structure refinement in CASP9.

Authors:  Justin L MacCallum; Alberto Pérez; Michael J Schnieders; Lan Hua; Matthew P Jacobson; Ken A Dill
Journal:  Proteins       Date:  2011-08-30

5.  Improved molecular replacement by density- and energy-guided protein structure optimization.

Authors:  Frank DiMaio; Thomas C Terwilliger; Randy J Read; Alexander Wlodawer; Gustav Oberdorfer; Ulrike Wagner; Eugene Valkov; Assaf Alon; Deborah Fass; Herbert L Axelrod; Debanu Das; Sergey M Vorobiev; Hideo Iwaï; P Raj Pokkuluri; David Baker
Journal:  Nature       Date:  2011-05-01       Impact factor: 49.962

6.  Predicting protein structures with a multiplayer online game.

Authors:  Seth Cooper; Firas Khatib; Adrien Treuille; Janos Barbero; Jeehyung Lee; Michael Beenen; Andrew Leaver-Fay; David Baker; Zoran Popović; Foldit Players
Journal:  Nature       Date:  2010-08-05       Impact factor: 49.962

Review 7.  Inhibitors of HIV-1 protease: current state of the art 10 years after their introduction. From antiretroviral drugs to antifungal, antibacterial and antitumor agents based on aspartic protease inhibitors.

Authors:  Antonio Mastrolorenzo; Stefano Rusconi; Andrea Scozzafava; Giuseppe Barbaro; Claudiu T Supuran
Journal:  Curr Med Chem       Date:  2007       Impact factor: 4.530

8.  CASP9 assessment of free modeling target predictions.

Authors:  Lisa Kinch; Shuo Yong Shi; Qian Cong; Hua Cheng; Yuxing Liao; Nick V Grishin
Journal:  Proteins       Date:  2011-10-14

9.  The HHpred interactive server for protein homology detection and structure prediction.

Authors:  Johannes Söding; Andreas Biegert; Andrei N Lupas
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  84 in total

1.  Algorithm discovery by protein folding game players.

Authors:  Firas Khatib; Seth Cooper; Michael D Tyka; Kefan Xu; Ilya Makedon; Zoran Popovic; David Baker; Foldit Players
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-07       Impact factor: 11.205

2.  Cardiovascular epidemiology in a changing world--challenges to investigators and the National Heart, Lung, and Blood Institute.

Authors:  Paul D Sorlie; Diane E Bild; Michael S Lauer
Journal:  Am J Epidemiol       Date:  2012-03-12       Impact factor: 4.897

3.  Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease.

Authors:  Mi Li; Alla Gustchina; Rui Cruz; Marisa Simões; Pedro Curto; Juan Martinez; Carlos Faro; Isaura Simões; Alexander Wlodawer
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-09-30

4.  Designing Videogames to Crowdsource Accelerometer Data Annotation for Activity Recognition Research.

Authors:  Aditya Ponnada; Seth Cooper; Binod Thapa-Chhetry; Josh Aaron Miller; Dinesh John; Stephen Intille
Journal:  Proc Annu Symp Comput Hum Interact Play       Date:  2019-10

Review 5.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

Review 6.  Crowdsourcing--harnessing the masses to advance health and medicine, a systematic review.

Authors:  Benjamin L Ranard; Yoonhee P Ha; Zachary F Meisel; David A Asch; Shawndra S Hill; Lance B Becker; Anne K Seymour; Raina M Merchant
Journal:  J Gen Intern Med       Date:  2013-07-11       Impact factor: 5.128

7.  Coarse-grained, foldable, physical model of the polypeptide chain.

Authors:  Promita Chakraborty; Ronald N Zuckermann
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-29       Impact factor: 11.205

8.  The quality and validation of structures from structural genomics.

Authors:  Marcin J Domagalski; Heping Zheng; Matthew D Zimmerman; Zbigniew Dauter; Alexander Wlodawer; Wladek Minor
Journal:  Methods Mol Biol       Date:  2014

9.  Crowdtruth validation: a new paradigm for validating algorithms that rely on image correspondences.

Authors:  Lena Maier-Hein; Daniel Kondermann; Tobias Roß; Sven Mersmann; Eric Heim; Sebastian Bodenstedt; Hannes Götz Kenngott; Alexandro Sanchez; Martin Wagner; Anas Preukschas; Anna-Laura Wekerle; Stefanie Helfert; Keno März; Arianeb Mehrabi; Stefanie Speidel; Christian Stock
Journal:  Int J Comput Assist Radiol Surg       Date:  2015-04-18       Impact factor: 2.924

10.  Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing.

Authors:  Willy Wriggers; Wilma K Olson; Cristobal G Dos Remedios
Journal:  Biophys Rev       Date:  2012-09-01
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