DescribePROT: database of amino acid-level protein structure and function predictions

Zhao, Bi; Katuwawala, Akila; Oldfield, Christopher J.; Dunker, A. Keith; Faraggi, Eshel; Gsponer, Jörg; Kloczkowski, Andrzej; Malhis, Nawar; Mirdita, Milot; Obradović, Zoran; Söding, Johannes; Steinegger, Martin; Zhou, Yaoqi; Kurgan, Lukasz

doi:10.1093/nar/gkaa931

Cited by 55 publications

(43 citation statements)

References 101 publications

(77 reference statements)

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“…This prompted us to investigate more proteins located at the NPC and its vicinity. For that purpose, we then took advantage of the DescribePROT database that provides access to pre-computed predictions from VSL2B for the Arabidopsis thaliana proteome (35). For the whole proteome, VSL2B predicts a median value of 36% of IDRs consistent with previous predictions (56).…”

Section: Resultsmentioning

confidence: 99%

“…VSL2B is the baseline predictor of VSL2 that is using only the amino-acid composition-based features that can be calculated directly from the protein sequence (34). DescribePROT database was used to collect pre-computed IDR predictions for 27,466 proteins of the Arabidopsis thaliana proteome including those predicted by VSL2B (35). VSL2B predictions were extracted for 31 NUPs, 5 Nucleoskeleton proteins and 5 inner nuclear membrane proteins ( Supplemental Table S3 ).…”

Section: Methodsmentioning

confidence: 99%

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Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

Mermet

Voisin

Mordier

et al. 2021

Preprint

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The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear morphology and gene expression. To understand how the Arabidopsis nucleoskeleton physically connects to the nuclear periphery, we investigated the nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. Computational predictions identified three evolutionary conserved peptide motifs within the N-terminal region of KAKU4. Functional analysis revealed that these motifs are required for homomerization of KAKU4, interaction with the nucleoskeleton proteins CROWDED NUCLEI (CRWN) and localization at the nuclear periphery. We find that similar protein motifs are present in NUP82 and NUP136, two plant specific nucleoporins from the Nuclear Pore Complex (NPC) basket. These conserved motifs allow the two nucleoporins to bind CRWN proteins, thus revealing a physical link between the nucleoskeleton and nuclear pores in plants. Finally, whilst NUP82, NUP136 and KAKU4 have a common evolutionary history predating non-vascular land plants, KAKU4 mainly localizes outside the NPC suggesting neofunctionalization of an ancient nucleoporin into a new nucleoskeleton component.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

Mermet

Voisin

Mordier

et al. 2021

Preprint

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“…Three additional databases, based on predictions of structure and disorder (discussed below), provide greatly expanded lists of likely IDPs, IDRs and their probable functions. These three databases are as follows: The Mobi Database ( http://protein.bio.unipd.it/mobi2/ [ 23 ]), The Database of Disordered Protein Prediction (D 2 P 2 , http://d2p2.pro [ 24 ]), and The DescribeProt Database ( http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/ [ 25 ]). …”

Section: Introductionmentioning

confidence: 99%

On the roles of intrinsically disordered proteins and regions in cell communication and signaling

2021

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For proteins, the sequence → structure → function paradigm applies primarily to enzymes, transmembrane proteins, and signaling domains. This paradigm is not universal, but rather, in addition to structured proteins, intrinsically disordered proteins and regions (IDPs and IDRs) also carry out crucial biological functions. For these proteins, the sequence → IDP/IDR ensemble → function paradigm applies primarily to signaling and regulatory proteins and regions. Often, in order to carry out function, IDPs or IDRs cooperatively interact, either intra- or inter-molecularly, with structured proteins or other IDPs or intermolecularly with nucleic acids. In this IDP/IDR thematic collection published in Cell Communication and Signaling, thirteen articles are presented that describe IDP/IDR signaling molecules from a variety of organisms from humans to fruit flies and tardigrades (“water bears”) and that describe how these proteins and regions contribute to the function and regulation of cell signaling. Collectively, these papers exhibit the diverse roles of disorder in responding to a wide range of signals as to orchestrate an array of organismal processes. They also show that disorder contributes to signaling in a broad spectrum of species, ranging from micro-organisms to plants and animals.

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“…Extending PASS to other prediction tasks in the future will also likely be aided by recent efforts to consolidate databases of sequences with pre-calculated predictions of various attributes from a range of tools. One such example being the residue-level predictions provided in DescribePROT 66 . As more of the protein universe is discovered the need for methods that are independent of homology only grows.…”

Section: Discussionmentioning

confidence: 99%

A Deep Semi-Supervised Framework for Accurate Modelling of Orphan Sequences

Moffat

Jones

2020

Preprint

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Predicting the secondary structure of a single protein sequence in the absence of homology information has remained a challenge for several decades. Although not as performant as their homology-based counterparts, single-sequence methods are not constrained by the requirement of evolutionary information. More accurate single-sequence approaches have the potential to improve structural modelling across the vast majority of sequence space, especially in areas of great scientific interest like viral proteins, the "dark proteome", and de novo protein design. Here we introduce S4PRED, the successor to the open-source PSIPRED-Single method, which utilizes semi-supervised learning to achieve a Q3 score of 75.3% on the standard CB513 test set, taking only single sequences as input. Not only does this result represent a leap in performance for single-sequence methods, it also provides a blueprint for the development of future tools, beyond waiting for larger structural datasets and more powerful neural networks.

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DescribePROT: database of amino acid-level protein structure and function predictions

Cited by 55 publications

References 101 publications

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

On the roles of intrinsically disordered proteins and regions in cell communication and signaling

A Deep Semi-Supervised Framework for Accurate Modelling of Orphan Sequences

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