Evidence map›Paper›PMID 38764597›Full record

ArticleArXiv2024

A Curated Rotamer Library for Common Post-Translational Modifications of Proteins.

Oufan Zhang, Shubhankar A Naik, Zi Hao Liu, Julie Forman-Kay, Teresa Head-Gordon

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PubMed Full text at PMC
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

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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

5 · Who and what money

Authors and funding

5 authors.

Oufan ZhangKenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
Shubhankar A NaikDepartment of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
Zi Hao LiuMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
Julie Forman-KayMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
Teresa Head-GordonKenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.

Funding

Calculating Ensembles of Discrete Dynamic Complexes and Condensed States of Intrinsically Disordered ProteinsR01GM127627 · UNIVERSITY OF CALIFORNIA BERKELEY · 2025 to 2025
$274k
NIGMS NIH HHS R01 GM127627
6 · The paper itself

Abstract

Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However much of protein function is modulated beyond the translated sequence through thFiguree introduction of post-translational modifications (PTMs). In this work we have provided a curated set of side chain rotamers for the most common PTMs derived from the RCSB PDB database, including phosphorylated, methylated, and acetylated sidechains. Our rotamer libraries improve upon existing methods such as SIDEpro and Rosetta in predicting the experimental structures for PTMs in folded proteins. In addition, we showcase our PTM libraries in full use by generating ensembles with the Monte Carlo Side Chain Entropy (MCSCE) for folded proteins, and combining MCSCE with the Local Disordered Region Sampling algorithms within IDPConformerGenerator for proteins with intrinsically disordered regions.

Identifiers

PMID38764597
PMCPMC11100909

What Socratic holds

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LicenceCC BY
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Registered trials

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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 Socratic graph.