Assessment of protein assembly prediction in CASP13

Proteins
Dmytro GuzenkoJose M Duarte

Abstract

We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches where subunits are modeled in the context of the assemblies they form.

References

Jun 1, 1991·Trends in Biochemical Sciences·D S Goodsell
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Aug 26, 1998·Folding & Design·C J TsaiR Nussinov
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·D S Goodsell, A J Olson
Jul 11, 2003·The EMBO Journal·Irene M A Nooren, Janet M Thornton
Jun 25, 2004·Nucleic Acids Research·David E KimDavid Baker
May 16, 2006·Acta Crystallographica. Section D, Biological Crystallography·Sergei RadaevPeter D Sun
Sep 27, 2007·Proteins·Ralf JauchNeil D Clarke
Sep 5, 2009·Proteins·Domenico CozzettoAnna Tramontano
Dec 10, 2009·PLoS Computational Biology·R SathyapriyaMichael Lappe
May 29, 2010·BMC Bioinformatics·Jose M DuarteMichael Lappe
Nov 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kosuke Hashimoto, Anna R Panchenko
Oct 18, 2011·Proteins·Valerio MarianiTorsten Schwede
Dec 21, 2011·Archives of Biochemistry and Biophysics·Trevor Selwood, Eileen K Jaffe
Mar 29, 2014·Science·Werner Kühlbrandt
Apr 25, 2015·Nucleic Acids Research·Eugene Krissinel
Dec 3, 2016·Nucleic Acids Research·Natalie L DawsonIan Sillitoe
Oct 27, 2017·Proteins·Joerg SchaarschmidtAlexandre M J J Bonvin
Oct 27, 2017·Proteins·Aleix LafitaGuido Capitani
Nov 12, 2017·Proteins·Marc F LensinkShoshana J Wodak
Dec 21, 2017·Journal of Molecular Biology·Lukas ZimmermannVikram Alva
May 1, 2018·PLoS Computational Biology·Spencer BlivenJose M Duarte
May 23, 2018·Nucleic Acids Research·Andrew WaterhouseTorsten Schwede
Feb 9, 2019·PLoS Computational Biology·Aleix LafitaJose M Duarte
Mar 21, 2019·Annual Review of Biomedical Engineering·Jana OgnjenovićSriram Subramaniam
Apr 10, 2019·Current Opinion in Structural Biology·Qifang Xu, Roland L Dunbrack
Jul 12, 2019·Proteins·Lisa N KinchNick V Grishin
Oct 7, 2019·Proteins·Rojan ShresthaAndras Fiser

❮ Previous
Next ❯

Citations

Oct 3, 2019·Proteins·Andriy KryshtafovychMaya Topf
Apr 3, 2020·PLoS Computational Biology·Yazan HaddadZbynek Heger
Nov 8, 2019·Proteins·Justas DapkūnasČeslovas Venclovas
Jun 9, 2021·Nature Communications·Sony MalhotraMaya Topf
May 25, 2021·Computational and Structural Biotechnology Journal·Megan EgbertSandor Vajda
May 23, 2021·Briefings in Bioinformatics·Luciano A Abriata, Matteo Dal Peraro
Jul 6, 2021·Journal of Molecular Biology·Liisa LutterWei-Feng Xue
Jan 31, 2020·Journal of Chemical Information and Modeling·Agnieszka S KarczyńskaCezary Czaplewski
Mar 7, 2020·Journal of Chemical Information and Modeling·Luciano A Abriata, Matteo Dal Peraro
Aug 23, 2021·Journal of Molecular Graphics & Modelling·Anna AntoniakKarolina Ziȩba
Aug 28, 2021·International Journal of Molecular Sciences·Aljaž Gaber, Miha Pavšič
Aug 3, 2021·Proteins·Burcu OzdenEzgi Karaca
Sep 1, 2021·Proteins·Andriy KryshtafovychUNKNOWN CASP-COVID participants
Nov 15, 2021·Journal of Molecular Biology·Martina MaritanDavid S Goodsell

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.