Literature DB >> 31569265

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13.

J Eduardo Fajardo1,2, Rojan Shrestha1,2, Nelson Gil1,2, Adam Belsom3, Silvia N Crivelli4, Cezary Czaplewski5, Krzysztof Fidelis6, Sergei Grudinin7, Mikhail Karasikov8,9,10, Agnieszka S Karczyńska5, Andriy Kryshtafovych6, Alexander Leitner11, Adam Liwo5,12, Emilia A Lubecka13, Bohdan Monastyrskyy6, Guillaume Pagès7, Juri Rappsilber2,14, Adam K Sieradzan5, Celina Sikorska5, Esben Trabjerg11, Andras Fiser1,2.   

Abstract

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.
© 2019 Wiley Periodicals, Inc.

Entities:  

Keywords:  CASP13; chemical crosslinking/mass spectrometry; chemical-crosslink-assisted protein structure modeling

Mesh:

Substances:

Year:  2019        PMID: 31569265      PMCID: PMC6851497          DOI: 10.1002/prot.25816

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  38 in total

1.  Reliability of assessment of protein structure prediction methods.

Authors:  Marc A Marti-Renom; M S Madhusudhan; András Fiser; Burkhard Rost; Andrej Sali
Journal:  Structure       Date:  2002-03       Impact factor: 5.006

2.  False discovery rate estimation for cross-linked peptides identified by mass spectrometry.

Authors:  Thomas Walzthoeni; Manfred Claassen; Alexander Leitner; Franz Herzog; Stefan Bohn; Friedrich Förster; Martin Beck; Ruedi Aebersold
Journal:  Nat Methods       Date:  2012-07-08       Impact factor: 28.547

3.  Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Authors:  Tadeusz L Ogorzalek; Greg L Hura; Adam Belsom; Kathryn H Burnett; Andriy Kryshtafovych; John A Tainer; Juri Rappsilber; Susan E Tsutakawa; Krzysztof Fidelis
Journal:  Proteins       Date:  2018-02-07

4.  Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.

Authors:  Mey Khalili; Adam Liwo; Anna Jagielska; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2005-07-21       Impact factor: 2.991

5.  Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.

Authors:  Emilia A Lubecka; Adam Liwo
Journal:  J Comput Chem       Date:  2019-04-29       Impact factor: 3.376

6.  Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

Authors:  Adam K Sieradzan; Rafał Jakubowski
Journal:  J Comput Chem       Date:  2017-01-11       Impact factor: 3.376

7.  Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

Authors:  Cezary Czaplewski; Sebastian Kalinowski; Adam Liwo; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2009-03-10       Impact factor: 6.006

8.  New statistical potential for quality assessment of protein models and a survey of energy functions.

Authors:  Dmitry Rykunov; Andras Fiser
Journal:  BMC Bioinformatics       Date:  2010-03-12       Impact factor: 3.169

9.  2016 update of the PRIDE database and its related tools.

Authors:  Juan Antonio Vizcaíno; Attila Csordas; Noemi Del-Toro; José A Dianes; Johannes Griss; Ilias Lavidas; Gerhard Mayer; Yasset Perez-Riverol; Florian Reisinger; Tobias Ternent; Qing-Wei Xu; Rui Wang; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2016-09-28       Impact factor: 16.971

10.  Quirks of Error Estimation in Cross-Linking/Mass Spectrometry.

Authors:  Lutz Fischer; Juri Rappsilber
Journal:  Anal Chem       Date:  2017-03-24       Impact factor: 6.986

View more
  8 in total

1.  Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.

Authors:  Adam K Sieradzan; Cezary Czaplewski; Paweł Krupa; Magdalena A Mozolewska; Agnieszka S Karczyńska; Agnieszka G Lipska; Emilia A Lubecka; Ewa Gołaś; Tomasz Wirecki; Mariusz Makowski; Stanisław Ołdziej; Adam Liwo
Journal:  Methods Mol Biol       Date:  2022

2.  Critical assessment of methods of protein structure prediction (CASP)-Round XIV.

Authors:  Andriy Kryshtafovych; Torsten Schwede; Maya Topf; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2021-10-07

3.  Assessment of protein assembly prediction in CASP13.

Authors:  Dmytro Guzenko; Aleix Lafita; Bohdan Monastyrskyy; Andriy Kryshtafovych; Jose M Duarte
Journal:  Proteins       Date:  2019-08-27

4.  Critical assessment of methods of protein structure prediction (CASP)-Round XIII.

Authors:  Andriy Kryshtafovych; Torsten Schwede; Maya Topf; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2019-10-23

Review 5.  Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.

Authors:  Mark R Chance; Erik R Farquhar; Sichun Yang; David T Lodowski; Janna Kiselar
Journal:  J Mol Biol       Date:  2020-02-21       Impact factor: 5.469

6.  Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.

Authors:  Agnieszka S Karczyńska; Karolina Ziȩba; Urszula Uciechowska; Magdalena A Mozolewska; Paweł Krupa; Emilia A Lubecka; Agnieszka G Lipska; Celina Sikorska; Sergey A Samsonov; Adam K Sieradzan; Artur Giełdoń; Adam Liwo; Rafał Ślusarz; Magdalena Ślusarz; Jooyoung Lee; Keehyoung Joo; Cezary Czaplewski
Journal:  J Chem Inf Model       Date:  2020-02-11       Impact factor: 4.956

Review 7.  Recent Developments in Data-Assisted Modeling of Flexible Proteins.

Authors:  Cezary Czaplewski; Zhou Gong; Emilia A Lubecka; Kai Xue; Chun Tang; Adam Liwo
Journal:  Front Mol Biosci       Date:  2021-12-24

8.  Decellularized nerve extracellular matrix/chitosan crosslinked by genipin to prepare a moldable nerve repair material.

Authors:  Fangsong Zhang; Naili Zhang; Qing Xu; Luping Zhang; Chunlei Zhang; Hongfu Liu; Zhenhai Yu; Shuai Zhou; Guoying Feng; Fei Huang
Journal:  Cell Tissue Bank       Date:  2021-06-11       Impact factor: 1.522

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.