Evidence map›Paper›PMID 39026849›Full record

ArticlebioRxiv : the preprint server for biology2024

Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.

Rituparna Samanta, Ameya Harmalkar, Priyamvada Prathima, Jeffrey J Gray

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

5 · Who and what money

Authors and funding

4 authors.

Rituparna SamantaDepartment of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-6804-7871
Ameya HarmalkarDepartment of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-6863-9634
Priyamvada PrathimaDepartment of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
Jeffrey J GrayDepartment of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-6380-2324

Funding

Prediction of the Structures of Protein ComplexesR35GM141881 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI JEFFREY J GRAY · 2021 to 2026
$7.6M
Prediction of the Structure of Therapeutic Antibodies with their AntigensR01GM078221 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GRAY, JEFFREY J · 2006 to 2020
$4.0M
NIGMS NIH HHS R01 GM078221NIGMS NIH HHS R35 GM141881
6 · The paper itself

Abstract

The oligomerization of protein macromolecules on cell membranes plays a fundamental role in regulating cellular function. From modulating signal transduction to directing immune response, membrane proteins (MPs) play a crucial role in biological processes and are often the target of many pharmaceutical drugs. Despite their biological relevance, the challenges in experimental determination have hampered the structural availability of membrane proteins and their complexes. Computational docking provides a promising alternative to model membrane protein complex structures. Here, we present Rosetta-MPDock, a flexible transmembrane (TM) protein docking protocol that captures binding-induced conformational changes. Rosetta-MPDock samples large conformational ensembles of flexible monomers and docks them within an implicit membrane environment. We benchmarked this method on 29 TM-protein complexes of variable backbone flexibility. These complexes are classified based on the root-mean-square deviation between the unbound and bound states (RMSD

Indexed as

backbone flexibilityenergy functionstransmembrane protein docking

Identifiers

PMID39026849
PMCPMC11257521

What Socratic holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.