Evidence map›Paper›PMID 28580454›Full record

ArticleFoundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)2016

A Discontinuous Potential Model for Protein-Protein Interactions.

Qing Shao, Carol K Hall

Abstract read
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In one paragraph

Article in Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

2 authors.

Qing ShaoDepartment of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh 27695, USA.
Carol K HallDepartment of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh 27695, USA.

Funding

Biotechnology Research Partnerships Renewal: Aggregation of Therapeutic ProteinsR01EB006006 · NIBIB · UNIVERSITY OF COLORADO · PI RANDOLPH, THEODORE W · 2006 to 2017
$7.2M
NIBIB NIH HHS R01 EB006006
6 · The paper itself

Abstract

Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.

Indexed as

Coarse-grained modelDiscontinuous molecular dynamicsOsmotic second virial coefficientProtein–protein interactionsSquare-well potential

Identifiers

PMID28580454
PMCPMC5453719

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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 OpenQuestion graph.