NUPACK: Analysis and Design of Nucleic Acid Systems

被引：1146

作者：

Zadeh, Joseph N. ^{[1
]}

Steenberg, Conrad D. ^{[1
]}

Bois, Justin S. ^{[1
]}

Wolfe, Brian R. ^{[1
]}

Pierce, Marshall B. ^{[1
]}

Khan, Asif R. ^{[1
]}

Dirks, Robert M. ^{[1
]}

Pierce, Niles A. ^{[1
,2
]}

机构：

[1] CALTECH, Dept Bioengn, Pasadena, CA 91125 USA

[2] CALTECH, Dept Appl & Computat Math, Pasadena, CA 91125 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2011年 / 32卷 / 01期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

RNA; DNA; complexes; concentrations; sequence design; BASE-PAIRING PROBABILITIES; THERMODYNAMIC PROPERTIES; INCLUDING PSEUDOKNOTS; SECONDARY STRUCTURE; RNA; PREDICTION; ALGORITHM;

D O I：

10.1002/jcc.21596

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 170-173, 2011

引用

页码：170 / 173

页数：4

共 11 条

[1] A partition function algorithm for nucleic acid secondary structure including pseudoknots [J].