RNA-Parafold: Algorithms and Web Server for Parametric Aspects of RNA Secondary Structure

波士顿学院被授予专注于RNA二级结构的新参数方面的赠款。具体地，针对与给定RNA序列的诱变剂、给定RNA结构的邻居、局部最优结构、具有发夹环的结构相关的参数化折叠问题，计算配分函数、碱基配对概率和统计有效的抽样结构的算法。所有算法的公开访问将通过一个名为RNA-Parafold的统一网络服务器提供，其中还将提供源代码。通过将重点放在不同于热力学平衡下的最小自由能或低能系综的RNA折叠方面，拟议的研究将对理解RNA、成核位置、折叠景观、具有所需折叠特性的RNA序列的设计、RNA构象开关的检测、顺式调控基序的检测以及基因表达微阵列中的靶探针杂交产生重大影响。将在RNA-Parafold中开发的工具将在结构生物学、计算化学和计算药物设计中得到更广泛的使用。波士顿学院提供的课程和培训机会将确保在本科生和研究生层面产生广泛影响，这些课程和培训机会为女性和少数族裔提供了特殊的机会。

Boston College is awarded a grant to focus on novel parametric aspects of RNA secondary structure. Specifically, algorithms to compute the partition function, base pairing probability, and statistically valid sampled structures for parameterized folding problems related to mutagens of a given RNA sequence, neighbors of a given RNA structure, locally optimal structures, structures having hairpin loops. Public access to all algorithms will be provided through a unified web server, to be called RNA-parafold, where source code will additionally be made available. By focusing on aspects of RNA folding distinct from those of minimum free energy or of the low energy ensemble at thermodynamic equilibrium, the proposed research will have significant impact on the understanding of RNA, nucleation sites, folding landscapes, design of RNA sequences having desired folding properties, detection of RNA conformational switches, detection of cis-regulatory motifs, and target-probe hybridization in gene expression microarrays. The tools to be developed in RNA-parafold will be of broader use to structural biology, computational chemistry and computational drug design. Broad impact at the undergraduate and graduate level will be ensured by courses and training opportunities offered at Boston College, which provide special opportunities for females and minorities.