Protein Structure-Based Prediction of Functional Information
基于蛋白质结构的功能信息预测
基本信息
- 批准号:0517292
- 负责人:
- 金额:--
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2005
- 资助国家:美国
- 起止时间:2005-08-01 至 2009-07-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
One of the most important tasks in genome research is to discover the function of the many gene products whose sequences are now known. Structural genomics efforts are rapidly increasing the number of known three-dimensional structures of these gene products, but the determination of function from the structure has proved to be difficult. The goals of this project are to develop and implement a methodology for the prediction of functional sites in proteins from their three-dimensional structures alone. This method will be fast, so that it can analyze structures on a high-throughput basis. The method will also be independent of any sequence or structure alignments or comparisons, so that it is applicable to proteins with few or no homologues, to novel folds, and to engineered structures. The method will begin with the titration curve analyses that have recently been developed by this group and tested specifically for functional site identification. Now these analyses will be coupled with other structure-based calculations, to identify catalytic and binding sites with high degree of accuracy and precision. In addition, hypotheses will be tested in order to understand the basis for the success of the method. The most significant element of intellectual merit of the proposed study is the development of a unique method to aid in the analysis and interpretation of structural genomics data. The ability to predict the function of gene products has broad impact in areas beyond molecular biology, including plant science, agriculture, and counter-bioterrorism efforts. The broader impact of this project includes the training of students, including students from underrepresented groups, at the interface of the biological, physical, and computational sciences. The project will be incorporated into the PI's outreach activities, which include ongoing efforts to promote careers in the sciences to minority youth, including undergraduates and K-12 students.
基因组研究中最重要的任务之一是发现许多基因产物的功能,这些基因产物的序列现在是已知的。 结构基因组学的努力正在迅速增加这些基因产物的已知三维结构的数量,但从结构中确定功能已被证明是困难的。该项目的目标是开发和实施一种仅从三维结构预测蛋白质功能位点的方法。这种方法将是快速的,因此它可以在高通量的基础上分析结构。该方法还将独立于任何序列或结构比对或比较,使得其适用于具有很少或没有同源物的蛋白质、新折叠和工程化结构。该方法将开始于滴定曲线分析,该分析是由该小组最近开发的,并专门用于功能位点鉴定。现在,这些分析将与其他基于结构的计算相结合,以高精度和高精度识别催化和结合位点。此外,还将对假设进行检验,以了解该方法成功的基础。 拟议研究的最重要的智力价值要素是开发了一种独特的方法来帮助分析和解释结构基因组学数据。预测基因产物功能的能力在分子生物学以外的领域具有广泛的影响,包括植物科学,农业和反生物恐怖主义工作。 该项目的更广泛影响包括在生物、物理和计算科学的界面上培训学生,包括来自代表性不足群体的学生。该项目将被纳入PI的外联活动,其中包括正在进行的向包括本科生和K-12学生在内的少数民族青年促进科学事业的努力。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Mary Jo Ondrechen其他文献
Distal Residues and Enzyme Activity: Implications for Personalized Medicine
- DOI:
10.1016/j.bpj.2019.11.2937 - 发表时间:
2020-02-07 - 期刊:
- 影响因子:
- 作者:
Lisa Ngu;Jenifer N. Winters;Lee Makowski;Penny J. Beuning;Mary Jo Ondrechen - 通讯作者:
Mary Jo Ondrechen
Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis
在创伤后骨关节炎的兔模型中,靶向软骨的阳离子肽载体显示出对软骨的深度渗透和滞留。
- DOI:
10.1016/j.joca.2025.04.001 - 发表时间:
2025-06-01 - 期刊:
- 影响因子:9.000
- 作者:
Timothy L. Boyer;Olivia Chao;Bill Hakim;Luke Childress;Quentin A. Meslier;Suhasini M. Iyengar;Mary Jo Ondrechen;Ryan M. Porter;Ambika G. Bajpayee - 通讯作者:
Ambika G. Bajpayee
Computed chemical properties for predicting protein function
- DOI:
10.1016/j.bpj.2021.11.2042 - 发表时间:
2022-02-11 - 期刊:
- 影响因子:
- 作者:
Suhasini Iyengar;Lakindu Pathira Kankanamge;Penny Beuning;Mary Jo Ondrechen - 通讯作者:
Mary Jo Ondrechen
Machine learning for prediction of protein function and elucidation of enzyme function and control
- DOI:
10.1016/j.bpj.2023.11.2608 - 发表时间:
2024-02-08 - 期刊:
- 影响因子:
- 作者:
Lakindu Pathira Kankanamge;Lydia A. Ruffner;Atif Shafique;Suhasini M. Iyengar;Kelly K. Barnsley;Penny Beuning;Mary Jo Ondrechen - 通讯作者:
Mary Jo Ondrechen
Potential energy surfaces for a mixed-valence dimer in an applied electric field
- DOI:
10.1007/bf01113540 - 发表时间:
1995-03-01 - 期刊:
- 影响因子:1.500
- 作者:
Leonel F. Murga;Mary Jo Ondrechen - 通讯作者:
Mary Jo Ondrechen
Mary Jo Ondrechen的其他文献
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{{ truncateString('Mary Jo Ondrechen', 18)}}的其他基金
Role of Coupled Amino Acids in the Mechanisms of Enzyme Catalysis
偶联氨基酸在酶催化机制中的作用
- 批准号:
2147498 - 财政年份:2022
- 资助金额:
-- - 项目类别:
Standard Grant
RAPID: Undergraduate Research in Modeling and Computation for Discovery of Molecular Probes for SARS-CoV-2 Proteins
RAPID:发现 SARS-CoV-2 蛋白分子探针的建模和计算本科生研究
- 批准号:
2031778 - 财政年份:2020
- 资助金额:
-- - 项目类别:
Standard Grant
RAPID: D3SC: Identification of Chemical Probes and Inhibitors Targeting Novel Sites on SARS-CoV-2 Proteins for COVID-19 Intervention
RAPID:D3SC:针对 SARS-CoV-2 蛋白新位点的化学探针和抑制剂的鉴定,用于干预 COVID-19
- 批准号:
2030180 - 财政年份:2020
- 资助金额:
-- - 项目类别:
Standard Grant
D3SC: Mining for mechanistic information to predict protein function
D3SC:挖掘机制信息来预测蛋白质功能
- 批准号:
1905214 - 财政年份:2019
- 资助金额:
-- - 项目类别:
Standard Grant
Distal Residues in Enzyme Catalysis and Protein Design
酶催化和蛋白质设计中的远端残基
- 批准号:
1517290 - 财政年份:2015
- 资助金额:
-- - 项目类别:
Standard Grant
Chemical Signatures for the Discovery of Protein Function
用于发现蛋白质功能的化学特征
- 批准号:
1305655 - 财政年份:2013
- 资助金额:
-- - 项目类别:
Standard Grant
Understanding Extended Active Sites in Enzymes
了解酶中的扩展活性位点
- 批准号:
1158176 - 财政年份:2012
- 资助金额:
-- - 项目类别:
Standard Grant
Are Enzyme Active Sites Built in Multiple Layers?
酶活性位点是多层构建的吗?
- 批准号:
0843603 - 财政年份:2009
- 资助金额:
-- - 项目类别:
Standard Grant
THEMATICS: Development and Application of a New Computational Tool for Functional Genomics
主题:功能基因组学新计算工具的开发和应用
- 批准号:
0135303 - 财政年份:2002
- 资助金额:
-- - 项目类别:
Standard Grant
POWRE: Enzyme-Substrate Interactions Mediated by Vitamin B6
POWRE:维生素 B6 介导的酶-底物相互作用
- 批准号:
0074574 - 财政年份:2000
- 资助金额:
-- - 项目类别:
Standard Grant
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