MultiCoil：一个用于预测双股和三股卷曲螺旋的程序。
MultiCoil: a program for predicting two- and three-stranded coiled coils.
作者信息
Wolf E, Kim P S, Berger B
机构信息
Howard Hughes Medical Institute, Whitehead Institute, MIT, Cambridge, Massachusetts 02142, USA.
出版信息
Protein Sci. 1997 Jun;6(6):1179-89. doi: 10.1002/pro.5560060606.
Abstract
A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two-stranded coiled-coil prediction program PairCoil to the identification of three-stranded coiled coils. The computations are based upon data gathered from a three-stranded coiled-coil database comprising 6,319 amino acid residues, as well as from the previously constructed two-stranded coiled-coil database. In addition to identifying coiled coils not predicted by the two-stranded database programs, MultiCoil accurately classifies the oligomerization states of known dimeric and trimeric coiled coils. Analysis of the MultiCoil scores provides insight into structural features of coiled coils, and yields estimates that 0.9% of all protein residues form three-stranded coiled coils and that 1.5% form two-stranded coiled coils. The MultiCoil program is available at http:/(/)theory.lcs.mit.edu/multicoil.
摘要
一种用于识别和区分三聚体和二聚体卷曲螺旋的新的多维评分方法已在MultiCoil程序中实现。该程序将双链卷曲螺旋预测程序PairCoil扩展到三链卷曲螺旋的识别。计算基于从包含6319个氨基酸残基的三链卷曲螺旋数据库以及先前构建的双链卷曲螺旋数据库收集的数据。除了识别双链数据库程序未预测到的卷曲螺旋外，MultiCoil还能准确地对已知的二聚体和三聚体卷曲螺旋的寡聚化状态进行分类。对MultiCoil评分的分析有助于深入了解卷曲螺旋的结构特征，并得出估计值，即所有蛋白质残基中有0.9%形成三链卷曲螺旋，1.5%形成双链卷曲螺旋。MultiCoil程序可在http:/(/)theory.lcs.mit.edu/multicoil获取。
相似文献
1
MultiCoil: a program for predicting two- and three-stranded coiled coils.MultiCoil：一个用于预测双股和三股卷曲螺旋的程序。
Protein Sci. 1997 Jun;6(6):1179-89. doi: 10.1002/pro.5560060606.
2
Comparative analysis of coiled-coil prediction methods.卷曲螺旋预测方法的比较分析。
J Struct Biol. 2006 Aug;155(2):140-5. doi: 10.1016/j.jsb.2006.03.009. Epub 2006 Mar 31.
3
Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.Multicoil2：在 twilight zone 中根据序列预测卷曲螺旋及其寡聚状态。
PLoS One. 2011;6(8):e23519. doi: 10.1371/journal.pone.0023519. Epub 2011 Aug 25.
4
Socket: a program for identifying and analysing coiled-coil motifs within protein structures.Socket：一个用于识别和分析蛋白质结构中卷曲螺旋基序的程序。
J Mol Biol. 2001 Apr 13;307(5):1427-50. doi: 10.1006/jmbi.2001.4545.
5
SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences.SCORER 2.0：一种用于区分平行二聚体和三聚体卷曲螺旋序列的算法。
Bioinformatics. 2011 Jul 15;27(14):1908-14. doi: 10.1093/bioinformatics/btr299. Epub 2011 May 16.
6
Effects of side-chain characteristics on stability and oligomerization state of a de novo-designed model coiled-coil: 20 amino acid substitutions in position "d".侧链特性对全新设计的模型卷曲螺旋的稳定性和寡聚化状态的影响：“d”位的20个氨基酸替换
J Mol Biol. 2000 Jul 7;300(2):377-402. doi: 10.1006/jmbi.2000.3866.
7
Predicting coiled coils by use of pairwise residue correlations.利用成对残基相关性预测卷曲螺旋。
Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8259-63. doi: 10.1073/pnas.92.18.8259.
8
AAFreqCoil: a new classifier to distinguish parallel dimeric and trimeric coiled coils.AAFreqCoil：一种用于区分平行二聚体和三聚体卷曲螺旋的新型分类器。
Mol Biosyst. 2015 Jul;11(7):1794-801. doi: 10.1039/c5mb00119f.
9
Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.22个蛋白质组的卷曲螺旋蛋白组成——亚细胞结构和运输控制中的差异与共同主题
BMC Evol Biol. 2005 Nov 16;5:66. doi: 10.1186/1471-2148-5-66.
10
The many types of interhelical ionic interactions in coiled coils - an overview.卷曲螺旋中的多种类型的螺旋间离子相互作用——概述。
J Struct Biol. 2010 May;170(2):192-201. doi: 10.1016/j.jsb.2010.03.003. Epub 2010 Mar 6.
引用本文的文献
1
Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences.从蛋白质序列预测二级和超二级结构的计算方法的最新进展
Methods Mol Biol. 2025;2870:1-19. doi: 10.1007/978-1-0716-4213-9_1.
2
Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway.TMED9 寡聚化和错误折叠蛋白货物在内质网早期分泌途径中捕获的分子基础。
Sci Adv. 2024 Sep 20;10(38):eadp2221. doi: 10.1126/sciadv.adp2221.
3
NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes.基于 NMR 的酵母 Oxa1-CTD 与核糖体相互作用的表征。
Int J Mol Sci. 2023 Sep 28;24(19):14657. doi: 10.3390/ijms241914657.
4
SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics.SPECC1L：一种调节胚胎组织动力学的细胞骨架蛋白。
Biochem Soc Trans. 2023 Jun 28;51(3):949-958. doi: 10.1042/BST20220461.
5
The motor domain of the kinesin Kip2 promotes microtubule polymerization at microtubule tips.动力域的驱动蛋白 Kip2 可促进微管末端的微管聚合。
J Cell Biol. 2023 Jul 3;222(7). doi: 10.1083/jcb.202110126. Epub 2023 Apr 24.
6
An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing.一个必需的 Noc3p 二聚化循环介导复制许可中的 ORC 双六聚体形成。
Life Sci Alliance. 2023 Jan 4;6(3). doi: 10.26508/lsa.202201594. Print 2023 Mar.
7
Conformational switch and multiple supramolecular structures of a newly identified self-assembling protein-mimetic peptide from YeaZ protein.来自YeaZ蛋白的新鉴定的自组装拟蛋白肽的构象转换和多种超分子结构
Front Chem. 2022 Dec 13;10:1038796. doi: 10.3389/fchem.2022.1038796. eCollection 2022.
8
Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta.感染戈登氏红杆菌噬菌体裂解盒中内溶素和类似孔蛋白的生物信息学特征。
PLoS One. 2022 Nov 17;17(11):e0276603. doi: 10.1371/journal.pone.0276603. eCollection 2022.
9
Identification and characterization of coiled-coil motifs across Autographa californica multiple nucleopolyhedrovirus genome.苜蓿银纹夜蛾多核型多角体病毒全基因组中卷曲螺旋基序的鉴定与特征分析
Heliyon. 2022 Sep 10;8(9):e10588. doi: 10.1016/j.heliyon.2022.e10588. eCollection 2022 Sep.
10
Protein Design: From the Aspect of Water Solubility and Stability.蛋白质设计：从水溶性和稳定性方面考虑。
Chem Rev. 2022 Sep 28;122(18):14085-14179. doi: 10.1021/acs.chemrev.1c00757. Epub 2022 Aug 3.
本文引用的文献
1
The spectrin repeat folds into a three-helix bundle in solution.血影蛋白重复序列在溶液中折叠成三螺旋束。
FEBS Lett. 1996 Apr 1;383(3):201-7. doi: 10.1016/0014-5793(96)00251-7.
2
A trimeric structural domain of the HIV-1 transmembrane glycoprotein.HIV-1跨膜糖蛋白的三聚体结构域。
Nat Struct Biol. 1995 Dec;2(12):1075-82. doi: 10.1038/nsb1295-1075.
3
Retrovirus envelope domain at 1.7 angstrom resolution.分辨率为1.7埃的逆转录病毒包膜结构域。
Nat Struct Biol. 1996 May;3(5):465-9. doi: 10.1038/nsb0596-465.
4
Predicting oligomerization states of coiled coils.预测卷曲螺旋的寡聚化状态。
Protein Sci. 1995 Aug;4(8):1596-607. doi: 10.1002/pro.5560040818.
5
Ionic interactions in the coiled-coil domain of laminin determine the specificity of chain assembly.层粘连蛋白卷曲螺旋结构域中的离子相互作用决定了链组装的特异性。
J Mol Biol. 1993 May 20;231(2):311-23. doi: 10.1006/jmbi.1993.1284.
6
S-laminin: mapping to mouse chromosome 9 and expression in the linked mutants tippy and ducky.S-层粘连蛋白：定位到小鼠9号染色体及在连锁突变体tippy和ducky中的表达
Genomics. 1993 Apr;16(1):278-81. doi: 10.1006/geno.1993.1178.
7
Regulation of heat shock factor trimer formation: role of a conserved leucine zipper.热休克因子三聚体形成的调控：保守亮氨酸拉链的作用。
Science. 1993 Jan 8;259(5092):230-4. doi: 10.1126/science.8421783.
8
Human laminin M chain (merosin): complete primary structure, chromosomal assignment, and expression of the M and A chain in human fetal tissues.人层粘连蛋白M链（merosin）：完整的一级结构、染色体定位以及M链和A链在人胎儿组织中的表达
J Cell Biol. 1994 Feb;124(3):381-94. doi: 10.1083/jcb.124.3.381.
9
A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants.GCN4亮氨酸拉链突变体中双股、三股和四股卷曲螺旋之间的转换。
Science. 1993 Nov 26;262(5138):1401-7. doi: 10.1126/science.8248779.
10
Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution.嗜热栖热菌丝氨酰 - tRNA合成酶在2.5埃分辨率下的精细晶体结构。
J Mol Biol. 1993 Nov 5;234(1):222-33. doi: 10.1006/jmbi.1993.1576.
Zotero 插件