Evidence map›Paper›PMID 18428869›Full record

ArticleCurrent protocols in nucleic acid chemistry2001

Molecular modeling of nucleic acid structure: setup and analysis.

T E Cheatham, B R Brooks, P A Kollman

Abstract read
In one paragraph

Article in Current protocols in nucleic acid chemistry, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

3 authors.

T E CheathamUniversity of Utah, Salt Lake City, Utah, USA.
B R Brooks
P A Kollman

Funding

Biomolecular simulation for the end-stage refinement of nucleic acid structureR01GM081411 · NIGMS · UNIVERSITY OF UTAH · PI CHEATHAM, THOMAS E. · 2008 to 2022
$2.7M
RNA-ligand interactions: simulation and experimentR01GM098102 · NIGMS · WASHINGTON UNIVERSITY · PI CHEATHAM, THOMAS E., HALL, KATHLEEN B · 2011 to 2014
$2.1M
NIGMS NIH HHS R01 GM081411NIGMS NIH HHS R01 GM098102
6 · The paper itself

Abstract

The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.

Indexed as

Models, MolecularNucleic Acid ConformationComputer SimulationNucleic AcidsThermodynamicsNucleic Acids

Identifiers

PMID18428869
PMCPMC4091932

What OpenQuestion holds

Textmetadata
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 OpenQuestion graph.