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Methods for estimation of model accuracy in CASP12
Stockholm Univ, Sweden.
Korea Inst Adv Study, South Korea.
Ben Gurion Univ Negev, Israel.
Korea Inst Adv Study, South Korea.
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2018 (English)In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 86, p. 361-373Article in journal (Refereed) Published
Abstract [en]

Methods to reliably estimate the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this article, the most successful groups in CASP12 describe their latest methods for estimates of model accuracy (EMA). We show that pure single model accuracy estimation methods have shown clear progress since CASP11; the 3 top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). Although the pure single model accuracy estimation methods outperform quasi-single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb-domain, and Wallner) in model selection, they are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact-based model quality measures (CAD, lDDT) the single model quality methods perform relatively better.

Place, publisher, year, edition, pages
WILEY , 2018. Vol. 86, p. 361-373
Keywords [en]
CASP; consensus predictions; estimates of model accuracy; machine learning; protein structure prediction; quality assessment
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:liu:diva-145749DOI: 10.1002/prot.25395ISI: 000425523000031PubMedID: 28975666OAI: oai:DiVA.org:liu-145749DiVA, id: diva2:1192521
Note

Funding Agencies|Swedish Research Council [VR-NT 2012-5046, 2012-5270]; Swedish e-Science Research Center; National Research Foundation of Korea (NRF) - Korea government (MEST) [2008-0061987]; Saudi Arabian Government; United States-Israel Binational Science Foundation (BSF) [2009432]; Israel Science Foundation (ISF) [1122/14]

Available from: 2018-03-22 Created: 2018-03-22 Last updated: 2018-05-06
In thesis
1. On protein structure, function and modularity from an evolutionary perspective
Open this publication in new window or tab >>On protein structure, function and modularity from an evolutionary perspective
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Om proteinstruktur, -function och modularitet ur en evolutionär synvinkel
Abstract [en]

We are compounded entities, given life by a complex molecular machinery. When studying these molecules we have to make sense of a diverse set of dynamical nanostructures with wast and intricate patterns of interactions. Protein polymers is one of the major groups of building blocks of such nanostructures which fold up into more or less distinct three dimensional structures. Due to their shape, dynamics and chemical properties proteins are able to perform a plethora of specific functions essential to all known cellular lifeforms.

The connection between protein sequence, translated into protein structure and in the continuation into protein function is well accepted but poorly understood. Malfunction in the process of protein folding is known to be implicated in natural aging, cancer and degenerative diseases such as Alzheimer's.

Protein folds are described hierarchically by structural ontologies such as SCOP, CATH and Pfam all which has yet to succeed in deciphering the natural language of protein function. These paradigmatic views centered on protein structure fail to describe more mutable entities, such as intrinsically disordered proteins (IDPs) which lack a clear defined structure.

As of 2012, about two thirds of cancer patients was predicted to survive past 5 years of diagnosis. Despite this, about a third do not survive and numerous of successfully treated patients suffer from secondary conditions due to chemotherapy, surgery and the like. In order to handle cancer more efficiently we have to better understand the underlying molecular mechanisms.

Elusive to standard methods of investigation, IDPs have a central role in pathology; dysfunction in IDPs are key factors in cellular system failures such as cancer, as many IDPs are hub regulators for major cell functions. These IDPs carry short conserved functional boxes, that are not described by known ontologies, which suggests the existence of a smaller entity. In an investigation of a pair of such boxes of c-MYC, a plausible structural model of its interacting with Pin1 emerged, but such a model still leaves the observer with a puzzle of understanding the actual function of that interaction.

If the protein is represented as a graph and modeled as the interaction patterns instead of as a structural entity, another picture emerges. As a graph, there is a parable from that of the boxes of IDPs, to that of sectors of allosterically connected residues and the theory of foldons and folding units. Such a description is also useful in deciphering the implications of specific mutations.

In order to render a functional description feasible for both structured and disordered proteins, there is a need of a model separate from form and structure. Realized as protein primes, patterns of interaction, which has a specific function that can be defined as prime interactions and context. With function defined as interactions, it might be possible that the discussion of proteins and their mechanisms is thereby simplified to the point rendering protein structural determination merely supplementary to understanding protein function.

Abstract [sv]

Människan byggs upp av celler, de i sin tur består av än mindre beståndsdelar; livets molekyler. Dessa fungerar som mekaniska byggstenar, likt maskiner och robotar som sliter vid fabrikens band; envar utförandes en absolut nödvändig funktion för cellens, och hela kroppens, fortsatta överlevnad. De av livets molekyler som beskrivs centralt i den här avhandling är proteiner, vilka i sin tur består utav en lång kedja, med olika typer av länkar, som likt garn lindar upp sig i ett nystan av en (mer eller mindre...) bestämd struktur som avgör dess roll och funktion i cellen.

Intrinsiellt oordnade proteiner (IDP) går emot denna enkla åskådning; de är proteiner som saknar struktur och beter sig mer likt spaghetti i vatten än en maskin. IDP är ändå funktionella och bär på centrala roller i cellens maskineri; exempel är oncoproteinet c-Myc som agerar "gaspedal" för cellen - fel i c-Myc's funktion leder till att cellerna löper amok, delar sig hejdlöst och vi får cancer.

Man har upptäckt att c-Myc har en ombytlig struktur vi inte kan se; studier av punktvisa förändringar, mutationer, i kedjan av byggstenar hos c-Myc visar att många länkar har viktiga roller i funktionen. Detta ger oss bättre förståelse om cancer men samtidigt är laboratoriearbetet både komplicerat och dyrt; här kan evolutionen vägleda oss och avslöja hemligheterna snabbare.

Molekylär evolution studeras genom att beräkna variation i proteinkedjan mellan besläktade arter som finns lagrade i databaser; detta visar snabbt, via nätverksanalys och grafteori, vilka delar av proteinet som är centrala och kopplade till varandra av nödvändighet för artens fortlevnad. På så vis hjälper evolutionen oss att förstå proteinfunktioner via modeller baserade på proteinernas interaktioner snarare än deras struktur.

Samma modeller kan nyttjas för att förstå dynamiska förlopp och skillnader mellan normala och patologiska varianter av proteiner; mutationer kan uppstå i vår arvsmassa som kan leda till sjukdom. Genom analys av proteinernas kopplingsnätverk i grafmodellerna kan man bättre förutsäga vilka mutationer som är farligare än andra. Dessutom har det visat sig att en sådan representation kan ge bättre förståelse för den normala funktionen hos ett protein än vad en proteinstruktur kan.

Här introduceras även konceptet proteinprimärer, vilket är en abstrakt representation av proteiner centrerad på deras interaktiva mönster, snarare än på partikulär form och struktur. Det är en förhoppning att en sådan representation skall förenkla diskussionen anbelangande proteinfunktion så till den grad att strukturbestämmelse av proteiner, som är en mycket kostsam och tidskrävande process, till viss mån kan anses vara sekundär i betydelse jämfört med funktionellt modellerande baserat på evolutionära data extraherade ur våra sekvensdatabaser.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2018. p. 77
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1914
Keywords
bioinformatics, structure, biology, intrinsical, disorder, protein, sequence, evolution, mutation, epistasis, function, allostery, dynamics, simulation, prediction, graph, network, bioinformatik, struktur, biologi, strukturbiologi, intrinsiellt, oordnad, protein, sekvens, evolution, mutation, epistasis, funktion, allosteri, dynamik, simulation, prediktion, graf, nätverk
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-147697 (URN)10.3384/diss.diva-147697 (DOI)9789176853474 (ISBN)
Public defence
2018-06-05, Planck, Hus F, Linköpings universitet, Linköping, 14:00 (English)
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Supervisors
Note

In the electronic version of the dissertation, the corrections from both errata lists have been carried out.

Available from: 2018-05-23 Created: 2018-05-06 Last updated: 2019-09-30Bibliographically approved

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