Opportunities and Challenges in RNA Structural Modeling and Design

Tamar Schlick, Anna Marie Pyle

Research output: Contribution to journalArticle

Abstract

We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.

Original languageEnglish (US)
JournalBiophysical Journal
DOIs
StateAccepted/In press - Oct 11 2016

Fingerprint

RNA
Databases
Complementary RNA
Nucleotide Motifs
Quality Control
Cluster Analysis
Software
Education
Research

ASJC Scopus subject areas

  • Biophysics

Cite this

Opportunities and Challenges in RNA Structural Modeling and Design. / Schlick, Tamar; Pyle, Anna Marie.

In: Biophysical Journal, 11.10.2016.

Research output: Contribution to journalArticle

@article{8e1e75e128694d4fab6209201d05e313,
title = "Opportunities and Challenges in RNA Structural Modeling and Design",
abstract = "We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.",
author = "Tamar Schlick and Pyle, {Anna Marie}",
year = "2016",
month = "10",
day = "11",
doi = "10.1016/j.bpj.2016.12.037",
language = "English (US)",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",

}

TY - JOUR

T1 - Opportunities and Challenges in RNA Structural Modeling and Design

AU - Schlick, Tamar

AU - Pyle, Anna Marie

PY - 2016/10/11

Y1 - 2016/10/11

N2 - We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.

AB - We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.

UR - http://www.scopus.com/inward/record.url?scp=85011277343&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85011277343&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2016.12.037

DO - 10.1016/j.bpj.2016.12.037

M3 - Article

C2 - 28162235

AN - SCOPUS:85011277343

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

ER -