使用几何不变指纹快速筛选蛋白质表面
Fast screening of protein surfaces using geometric invariant fingerprints.
作者信息
Yin Shuangye, Proctor Elizabeth A, Lugovskoy Alexey A, Dokholyan Nikolay V
机构信息
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Genetics Medicine, 120 Mason Farm Road, Chapel Hill, NC 27599-7260, USA.
出版信息
Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16622-6. doi: 10.1073/pnas.0906146106. Epub 2009 Sep 17.
Abstract
We develop a rapid and efficient method for the comparison of protein local surface similarities using geometric invariants (fingerprints). By combining fast fingerprint comparison with explicit alignment, we successfully screen the entire Protein Data Bank for proteins that possess local surface similarities. Our method is independent of sequence and fold similarities, and has potential application to protein structure annotation and protein-protein interface design.
摘要
我们开发了一种快速有效的方法，用于使用几何不变量（指纹）比较蛋白质局部表面相似性。通过将快速指纹比较与显式比对相结合，我们成功地在整个蛋白质数据库中筛选出具有局部表面相似性的蛋白质。我们的方法独立于序列和折叠相似性，在蛋白质结构注释和蛋白质-蛋白质界面设计方面具有潜在应用。
相似文献
1
Fast screening of protein surfaces using geometric invariant fingerprints.使用几何不变指纹快速筛选蛋白质表面
Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16622-6. doi: 10.1073/pnas.0906146106. Epub 2009 Sep 17.
2
3
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.利用几何深度学习破译蛋白质分子表面的相互作用指纹。
Nat Methods. 2020 Feb;17(2):184-192. doi: 10.1038/s41592-019-0666-6. Epub 2019 Dec 9.
4
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment.ProBiS 算法通过局部结构比对检测结构相似的蛋白质结合位点。
Bioinformatics. 2010 May 1;26(9):1160-8. doi: 10.1093/bioinformatics/btq100. Epub 2010 Mar 19.
5
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.蛋白质功能表面：配体结合位点的全局形状匹配和局部空间比对
BMC Struct Biol. 2008 Oct 27;8:45. doi: 10.1186/1472-6807-8-45.
6
Protein structure alignment and fast similarity search using local shape signatures.使用局部形状特征进行蛋白质结构比对和快速相似性搜索。
J Bioinform Comput Biol. 2004 Mar;2(1):215-39. doi: 10.1142/s0219720004000533.
7
LGA: A method for finding 3D similarities in protein structures.LGA：一种在蛋白质结构中寻找三维相似性的方法。
Nucleic Acids Res. 2003 Jul 1;31(13):3370-4. doi: 10.1093/nar/gkg571.
8
Encoding protein-ligand interaction patterns in fingerprints and graphs.编码蛋白质-配体相互作用模式的指纹和图。
J Chem Inf Model. 2013 Mar 25;53(3):623-37. doi: 10.1021/ci300566n. Epub 2013 Mar 6.
9
Fingerprint-based structure retrieval using electron density.基于电子密度的指纹结构检索。
Proteins. 2011 Mar;79(3):1002-9. doi: 10.1002/prot.22941. Epub 2011 Jan 3.
10
Protein interface conservation across structure space.蛋白质界面在结构空间中的保守性。
Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10896-901. doi: 10.1073/pnas.1005894107. Epub 2010 Jun 1.
引用本文的文献
1
A Complementarity-Based Approach to De Novo Binder Design.一种基于互补性的全新结合物设计方法。
Adv Sci (Weinh). 2025 Sep;12(33):e02015. doi: 10.1002/advs.202502015. Epub 2025 Jul 21.
2
Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features.利用AlphaFold2预测结构和表面特征的多模态几何学习用于抗菌肽鉴定
Brief Bioinform. 2025 May 1;26(3). doi: 10.1093/bib/bbaf261.
3
Targeting protein-ligand neosurfaces with a generalizable deep learning tool.使用通用深度学习工具靶向蛋白质-配体新表面。
Nature. 2025 Mar;639(8054):522-531. doi: 10.1038/s41586-024-08435-4. Epub 2025 Jan 15.
4
NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide-human leukocyte antigen complexes.NeoaPred：一种基于肽-人类白细胞抗原复合物的表面和结构特征预测免疫原性新抗原的深度学习框架。
Bioinformatics. 2024 Sep 2;40(9). doi: 10.1093/bioinformatics/btae547.
5
Leveraging Artificial Intelligence for Synergies in Drug Discovery: From Computers to Clinics.利用人工智能实现药物发现协同增效：从计算机到临床。
Curr Pharm Des. 2024;30(28):2187-2205. doi: 10.2174/0113816128308066240529121148.
6
PLO3S: Protein LOcal Surficial Similarity Screening.PLO3S：蛋白质局部表面相似性筛选
Comput Struct Biotechnol J. 2023 Dec 11;26:1-10. doi: 10.1016/j.csbj.2023.12.002. eCollection 2024 Dec.
7
Whole proteome mapping of compound-protein interactions.化合物-蛋白质相互作用的全蛋白质组图谱绘制。
Curr Res Chem Biol. 2022;2. doi: 10.1016/j.crchbi.2022.100035. Epub 2022 Sep 12.
8
ProteinMAE: masked autoencoder for protein surface self-supervised learning.蛋白质 MAE：用于蛋白质表面自监督学习的掩蔽自动编码器。
Bioinformatics. 2023 Dec 1;39(12). doi: 10.1093/bioinformatics/btad724.
9
De novo design of protein interactions with learned surface fingerprints.从头设计具有学习到的表面指纹的蛋白质相互作用。
Nature. 2023 May;617(7959):176-184. doi: 10.1038/s41586-023-05993-x. Epub 2023 Apr 26.
10
GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning.GeoBind：利用几何深度学习对蛋白质表面的核酸结合界面进行分割。
Nucleic Acids Res. 2023 Jun 9;51(10):e60. doi: 10.1093/nar/gkad288.
本文引用的文献
1
Fast protein tertiary structure retrieval based on global surface shape similarity.基于全局表面形状相似性的快速蛋白质三级结构检索
Proteins. 2008 Sep;72(4):1259-73. doi: 10.1002/prot.22030.
2
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.用于探索功能关系的蛋白质-配体结合位点的折叠独立结构比较。
J Mol Biol. 2006 Feb 3;355(5):1112-24. doi: 10.1016/j.jmb.2005.11.044. Epub 2005 Dec 1.
3
A fourier fingerprint-based method for protein surface representation.一种基于傅里叶指纹的蛋白质表面表示方法。
J Chem Inf Model. 2005 May-Jun;45(3):696-707. doi: 10.1021/ci049647j.
4
TM-align: a protein structure alignment algorithm based on the TM-score.TM-align：一种基于TM分数的蛋白质结构比对算法。
Nucleic Acids Res. 2005 Apr 22;33(7):2302-9. doi: 10.1093/nar/gki524. Print 2005.
5
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.作为蛋白质结合口袋和配体比较的3D形状描述符的实球谐展开系数
Bioinformatics. 2005 May 15;21(10):2347-55. doi: 10.1093/bioinformatics/bti337. Epub 2005 Feb 22.
6
Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching.迈向蛋白质 - 核苷酸复合物中磷酸结合位点的结构分类：使用几何匹配的自动化全对全结构比较。
Proteins. 2004 Aug 1;56(2):250-60. doi: 10.1002/prot.20123.
7
Recognition of functional sites in protein structures.蛋白质结构中功能位点的识别。
J Mol Biol. 2004 Jun 4;339(3):607-33. doi: 10.1016/j.jmb.2004.04.012.
8
Inferring functional relationships of proteins from local sequence and spatial surface patterns.从局部序列和空间表面模式推断蛋白质的功能关系。
J Mol Biol. 2003 Sep 12;332(2):505-26. doi: 10.1016/s0022-2836(03)00882-9.
9
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.利用分子表面数据库eF-site通过相似性搜索鉴定蛋白质生化功能。
Protein Sci. 2003 Aug;12(8):1589-95. doi: 10.1110/ps.0368703.
10
A new method to detect related function among proteins independent of sequence and fold homology.一种独立于序列和折叠同源性来检测蛋白质间相关功能的新方法。
J Mol Biol. 2002 Oct 18;323(2):387-406. doi: 10.1016/s0022-2836(02)00811-2.
Zotero 插件