Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.

Zi Hao Liu, Maria Tsanai, Oufan Zhang, Julie Forman-Kay, Teresa Head-Gordon

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In one paragraph

Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Zi Hao LiuMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

Maria TsanaiKenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.

Oufan ZhangKenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.

Julie Forman-KayMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

Teresa Head-GordonKenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.

Funding

Calculating Ensembles of Discrete Dynamic Complexes and Condensed States of Intrinsically Disordered ProteinsR01GM127627 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Teresa L. Head-Gordon · 2018 to 2026

$2.1M

NIGMS NIH HHS R01 GM127627

6 · The paper itself

Abstract

In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate structural and dynamic characteristics of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). Unlike crystallographic beamlines and their role in streamlining acquisition of structures for folded proteins, an integrated experimental and computational approach aimed at IDPs/IDRs has emerged. In this Perspective we aim to provide a robust overview of current computational tools for IDPs and IDRs, and most recently their complexes and phase separated states, including statistical models, physics-based approaches, and machine learning methods that permit structural ensemble generation and validation against many solution experimental data types.

Identifiers

PMID39279844

PMCPMC11398552

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.