Paircoil2: improved prediction of coiled coils from sequence.
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Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled–coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure. Availability: Paircoil2 is freely available as a web application and for download at Contact: keating@mit.edu; bab@mit.edu Supplementary information: Available at Bioinformatics online and at the Paircoil website.
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A new coiled-coil database of 1279 dimers and 333 trimers is derived from three sources: the Paircoil2 training set, coiled coils detected in the PDB using SOCKET, and new coiled-coil families described in the literature.
“A new coiled-coil database of 1279 dimers and 333 trimers is derived from three sources: the Paircoil2 training set [9], coiled coils detected in the PDB using SOCKET, and new coiled-coil families described in the literature.”
From Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011) · cites this paper as [9]
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Predicting coiled coils from protein sequences.
Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953 · see citing works
Core Structure of gp41 from the HIV Envelope Glycoprotein
Chan, D. C., Fass, D., Berger, J. M., & Kim, P. S. (1997) · Cell · doi:10.1016/s0092-8674(00)80205-6 · Cited by 1,961 · see citing works
Enlarged representative set of protein structures
Hobohm, U., & Sander, C. (1994) · Protein Science · doi:10.1002/pro.5560030317 · Cited by 788 · see citing works
Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy
Yonekura, K., Maki-Yonekura, S., & Namba, K. (2003) · Nature · doi:10.1038/nature01830 · Cited by 764 · see citing works
MultiCoil: A program for predicting two‐and three‐stranded coiled coils
Wolf, E., Kim, P. S., & Berger, B. (1997) · Protein Science · doi:10.1002/pro.5560060606 · Cited by 720 · see citing works
Self-citationPredicting coiled coils by use of pairwise residue correlations.
Berger, B., Wilson, D. B., Wolf, E., Tonchev, T., Milla, M. E., & Kim, P. S. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.18.8259 · Cited by 622 · see citing works
Self-citationPQS: a protein quaternary structure file server
Henrick, K. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01253-5 · Cited by 540 · see citing works
Tolerating some redundancy significantly speeds up clustering of large protein databases
Li, W.-Z., Jaroszewski, L., & Godzik, A. (2002) · Bioinform. · doi:10.1093/bioinformatics/18.1.77 · Cited by 517 · see citing works
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
Delorenzi, M., & Speed, T. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.4.617 · Cited by 479 · see citing works
Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays
Newman, J. R. S., & Keating, A. E. (2003) · Science · doi:10.1126/science.1084648 · Cited by 449 · see citing works
Self-citationWalshaw, J., & Woolfson, D. N. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4545 · Cited by 357 · see citing works
An extended microtubule-binding structure within the dynein motor domain
Gee, M. A., Heuser, J. E., & Vallee, R. B. (1997) · Nature · doi:10.1038/37663 · Cited by 292 · see citing works
Molecular architecture of intermediate filaments
Strelkov, S. V., Herrmann, H. O., & Aebi, U. (2003) · BioEssays · doi:10.1002/bies.10246 · Cited by 257 · see citing works
Singh, M., Berger, B., & Kim, P. S. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2796 · Cited by 145 · see citing works
Self-citationPredicting specificity in bZIP coiled-coil protein interactions
Fong, J. H., Keating, A. E., & Singh, M. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r11 · Cited by 111 · see citing works
Self-citationB-ZIP Proteins Encoded by the Drosophila Genome: Evaluation of Potential Dimerization PartnersPreprint
Fassler, J. S., Landsman, D., Acharya, A., Moll, J. R., Bonovich, M. T., & Vinson, C. (2002) · Genome Research · doi:10.1101/gr.67902 · Cited by 75 · see citing works
Morii, H., Takenawa, T., Arisaka, F., & Shimizu, T. (1997) · Biochemistry · doi:10.1021/bi962392l · Cited by 59 · see citing works
The Coiled-Coil Helix in the Neck of Kinesin
Thormählen, M., Marx, A., Sack, S., & Mandelkow�, E. (1998) · Journal of Structural Biology · doi:10.1006/jsbi.1998.3986 · Cited by 42 · see citing works
Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors
Vincentz, M., Schlögl, P. S., Corrêa, L. G. G., Kühne, F., & Leite, A. (2001) · Genetics and Molecular Biology · doi:10.1590/s1415-47572001000100009 · Cited by 10 · see citing works
Flagged first, then by citations
1 of the 22 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Genome sequence and analysis of the tuber crop potato
Xu, X., Pan, S., Cheng, S., Zhang, B., Mu, D., Ni, P., Zhang, G., Guzman, F., Torres, M., Lozano, R., et al. (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,050 · see citing works
The genome of the pear ( Pyrus bretschneideri Rehd.)Preprint
Wu, J., Wang, Z., Shi, Z., Zhang, S., Ming, R., Zhu, S., Khan, M. A., Tao, S., Korban, S. S., Wang, H., et al. (2012) · Genome Research · doi:10.1101/gr.144311.112 · Cited by 1,049 · see citing works
Argout, X., Salse, J., Aury, J., Guiltinan, M. J., Droc, G., Gouzy, J., Allègre, M., Chaparro, C., Legavre, T., Maximova, S. N., et al. (2010) · Nature Genetics · doi:10.1038/ng.736 · Cited by 745 · see citing works
The pangenome of an agronomically important crop plant Brassica oleracea
Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H. R., Martinez, P. A., Chan, C. K., Severn‐Ellis, A. A., McCombie, W. R., Parkin, I. A. P., et al. (2016) · Nature Communications · doi:10.1038/ncomms13390 · Cited by 543 · see citing works
Learning the protein language: Evolution, structure, and function
Bepler, T., & Berger, B. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.017 · Cited by 483 · see citing works
Self-citationFormation of starch in plant cells
Pfister, B., & Zeeman, S. C. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2250-x · Cited by 422 · see citing works
LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins
Sosa, B. A., Rothballer, A., Kutay, U., & Schwartz, T. (2012) · Cell · doi:10.1016/j.cell.2012.03.046 · Cited by 404 · see citing works
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
de Weyer, A.-L. V., Monteiro, F., Furzer, O. J., Nishimura, M. T., Çevik, V., Witek, K., Jones, J. D. G., Dangl, J. L., Weigel, D., & Bemm, F. (2019) · Cell · doi:10.1016/j.cell.2019.07.038 · Cited by 382 · see citing works
Zhang, G., Xu, Q., Bian, C., Tsai, W., Yeh, C., Liu, K.-W., Yoshida, K., Zhang, L., Chang, S., Chen, F., et al. (2016) · Scientific Reports · doi:10.1038/srep19029 · Cited by 350 · see citing works
Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Wang, L., Sheng, Y., Tong, C., Zhao, Y., Liu, Y., Song, C., Zhang, Y., Zhang, X., Wang, Y., Hua, W., et al. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r39 · Cited by 340 · see citing works
Protein Design: From the Aspect of Water Solubility and Stability
Qing, R., Hao, S., Smorodina, E., Jin, D., Zalevsky, A. O., & Zhang, S. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00757 · Cited by 321 · see citing works
Identification and localisation of the NB-LRR gene family within the potato genome
Jupe, F., Pritchard, L., Etherington, G., Mackenzie, K., Cock, P., Wright, F., Sharma, S. K., Bolser, D. M., Bryan, G. J., Jones, J. D. G., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-75 · Cited by 310 · see citing works
Structural specificity in coiled-coil interactions
Grigoryan, G., & Keating, A. E. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.04.008 · Cited by 290 · see citing works
Self-citationLee, S., Song, M., Seo, Y., Kim, H.-K., Ko, S., Cao, P., Suh, J.-P., Yi, G., Roh, J., Lee, S., et al. (2009) · Genetics · doi:10.1534/genetics.108.099226 · Cited by 280 · see citing works
Bujalka, H., Koenning, M., Jackson, S., Perreau, V. M., Pope, B., Hay, C. M., Mitew, S., Hill, A. F., Lu, Q. R., Wegner, M., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001625 · Cited by 271 · see citing works
“The UniProt mouse MYRF sequence (accession number Q3UR85) was submitted to several subcellular targeting motif and feature predictors including ELM [46], PSORTII [47], NucPred [48], TMPRED [49], HMMTOP [50], Das-TMfilter [51], Toppred II [52], Paircoil2 [53], and to the protein databases PFAM [54] and Prosite [55].”
MethodSreA‐mediated iron regulation in Aspergillus fumigatus
Schrettl, M., Kim, H. S., Eisendle, M., Kragl, C., Nierman, W. C., Heinekamp, T., Werner, E. R., Jacobsen, I. D., Illmer, P., Yi, H., et al. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06376.x · Cited by 264 · see citing works
Essential role of coiled-coils for aggregation and activity of Q/N-rich prions and polyQ proteins
Fiumara, F., Fioriti, L., Kandel, E., & Hendrickson, W. (2010) · Cell · doi:10.1016/j.cell.2010.11.042 · Cited by 249 · see citing works
Zhai, C., Lin, F., Dong, Z., He, X., Yuan, B., Zeng, X., Wang, L., & Pan, Q. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03462.x · Cited by 252 · see citing works
Monteiro, F., & Nishimura, M. T. (2018) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-080417-045817 · Cited by 212 · see citing works
A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing
Zhu, Y., Rowley, M. J., Böhmdorfer, G., & Wierzbicki, A. T. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.011 · Cited by 209 · see citing works
Yuan, B., Zhai, C., Wang, W., Zeng, X., Xu, X., Hu, H., Lin, F., Wang, L., & Pan, Q. (2010) · Theoretical and Applied Genetics · doi:10.1007/s00122-010-1506-3 · Cited by 206 · see citing works
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Billington, N., Wang, A., Mao, J., Adelstein, R. S., & Sellers, J. R. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.499848 · Cited by 203 · see citing works
Mutations in Centrosomal Protein CEP152 in Primary Microcephaly Families Linked to MCPH4
Guernsey, D. L., Jiang, H., Hussin, J., Arnold, M., Bouyakdan, K., Perry, S., Babineau-Sturk, T., Beis, J., Dumas, N., Evans, S. C., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.06.003 · Cited by 200 · see citing works
Evolution and function of CAG/polyglutamine repeats in protein–protein interaction networks
Schaefer, M. H., Wanker, E. E., & Andrade-Navarro, M. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks011 · Cited by 200 · see citing works
Identification and distribution of the NBS-LRR gene family in the Cassava genome
Lozano, R. D., Hamblin, M. T., Prochnik, S. E., & Jannink, J. (2015) · BMC Genomics · doi:10.1186/s12864-015-1554-9 · Cited by 194 · see citing works
Antony, D., Becker-Heck, A., Zariwala, M. A., Schmidts, M., Onoufriadis, A., Forouhan, M., Wilson, R., Taylor-Cox, T., Dewar, A. L., Jackson, C. L., et al. (2012) · Human Mutation · doi:10.1002/humu.22261 · Cited by 191 · see citing works
Halfmann, R., Alberti, S., Krishnan, R., Lyle, N. J., O'Donnell, C. W., King, O. D., Berger, B., Pappu, R. V., & Lindquist, S. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.013 · Cited by 179 · see citing works
Self-citationLiu, B., Persons, L., Lee, L., & de Boer, P. A. J. (2014) · Molecular Microbiology · doi:10.1111/mmi.12906 · Cited by 164 · see citing works
Yu, J., Tehrim, S., Zhang, F., Tong, C., Huang, J., Cheng, X., Dong, C., Zhou, Y. R., Qin, R., Hua, W., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-3 · Cited by 174 · see citing works
Assembly of synaptic active zones requires phase separation of scaffold molecules
McDonald, N. A., Fetter, R. D., & Shen, K. (2020) · Nature · doi:10.1038/s41586-020-2942-0 · Cited by 162 · see citing works
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Porter, B. W., Paidi, M. D., Ming, R., Alam, M. S., Nishijima, W. T., & Zhu, Y. J. (2009) · Molecular Genetics and Genomics · doi:10.1007/s00438-009-0434-x · Cited by 170 · see citing works
The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis
Qin, G., Xu, C., Ming, R., Tang, H., Guyot, R., Kramer, E. M., Hu, Y., Yi, X., Qi, Y., Xu, X., et al. (2017) · The Plant Journal · doi:10.1111/tpj.13625 · Cited by 170 · see citing works
Comparative analysis of coiled-coil prediction methods
Gruber, M., Söding, J., & Lupas, A. N. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.03.009 · Cited by 161 · see citing works
An endosomal tether undergoes an entropic collapse to bring vesicles together
Murray, D. H., Jahnel, M., Lauer, J. L., Avellaneda, M. J., Brouilly, N., Cezanne, A., Morales-Navarrete, H. A., Perini, E. D., Ferguson, C., Lupas, A. N., et al. (2016) · Nature · doi:10.1038/nature19326 · Cited by 161 · see citing works
CC+: a relational database of coiled-coil structures
Testa, O. D., Moutevelis, E., & Woolfson, D. N. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn675 · Cited by 158 · see citing works
Ji, H., Kim, S., Kim, Y.-H., Suh, J.-P., Park, H.-M., Sreenivasulu, N., Misra, G., Kim, S., Hechanova, S. L., Kim, H., et al. (2016) · Scientific Reports · doi:10.1038/srep34376 · Cited by 155 · see citing works
Pi64, Encoding a Novel CC-NBS-LRR Protein, Confers Resistance to Leaf and Neck Blast in Rice
Ma, J., Lei, C., Xu, X., Hao, K., Wang, J., Cheng, Z., Ma, X., Ma, J., Zhou, K., Zhang, X., et al. (2015) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-11-14-0367-r · Cited by 150 · see citing works
Coiled-Coil Design: Updated and Upgraded
Woolfson, D. N. (2017) · Subcellular Biochemistry · doi:10.1007/978-3-319-49674-0_2 · Cited by 149 · see citing works
Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae
Jaskólska, M., Adams, D. W., & Blokesch, M. (2022) · Nature · doi:10.1038/s41586-022-04546-y · Cited by 134 · see citing works
Zhang, M., Zhang, B., Qian, Q., Yu, Y., Li, R., Zhang, J., Liu, X., Zeng, D., Li, J., & Zhou, Y. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04238.x · Cited by 148 · see citing works
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Lau, N., Makita, Y., Kawashima, M., Taylor, T. D., Kondo, S., Othman, A. S., Shu‐Chien, A. C., & Matsui, M. (2016) · Scientific Reports · doi:10.1038/srep28594 · Cited by 148 · see citing works
De novo design of synthetic prion domains
Toombs, J. A., Petri, M., Paul, K. R., Kan, G. Y., Ben‐Hur, A., & Ross, E. D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119366109 · Cited by 143 · see citing works
New currency for old rope: from coiled-coil assemblies to α-helical barrels
Woolfson, D. N., Bartlett, G. J., Bruning, M., & Thomson, A. R. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.03.002 · Cited by 138 · see citing works
DISC1: Structure, Function, and Therapeutic Potential for Major Mental Illness
Soares, D. C., Carlyle, B. C., Bradshaw, N. J., & Porteous, D. J. (2011) · ACS Chemical Neuroscience · doi:10.1021/cn200062k · Cited by 129 · see citing works
New insights into the phylogenetic distribution and evolutionary origins of the septins
Nishihama, R., Onishi, M., & Pringle, J. R. (2011) · Biological Chemistry · doi:10.1515/bc.2011.086 · Cited by 129 · see citing works
Molecular dissection of IZUMO1, a sperm protein essential for sperm-egg fusion
Inoue, N., Hamada, D., Kamikubo, H., Hirata, K., Kataoka, M., Yamamoto, M., Ikawa, M., Okabe, M., & Hagihara, Y. (2013) · Development · doi:10.1242/dev.094854 · Cited by 127 · see citing works
X-ray Crystal Structure of a TRPM Assembly Domain Reveals an Antiparallel Four-stranded Coiled-coil
Fujiwara, Y., & Minor, D. L. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.08.059 · Cited by 122 · see citing works
Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases.
Djuranovic, S., Hartmann, M., Habeck, M., Ursinus, A., Zwickl, P., Martin, J., Lupas, A., & Zeth, K. (2009) · Molecules and Cells · doi:10.1016/j.molcel.2009.04.030 · Cited by 123 · see citing works
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Gertler, F. B., & Condeelis, J. S. (2010) · Trends in Cell Biology · doi:10.1016/j.tcb.2010.10.001 · Cited by 121 · see citing works
Wu, S., Shamimuzzaman, M., Sun, H., Salse, J., Sui, X., Wilder, A., Wu, Z., Levi, A., Xu, Y., Ling, K., et al. (2017) · The Plant Journal · doi:10.1111/tpj.13722 · Cited by 120 · see citing works
Lozano, R. D., Ponce, O., Ramirez, M., Mostajo, N., & Orjeda, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034775 · Cited by 120 · see citing works
The Structure and Topology of α-Helical Coiled Coils
Lupas, A. N., Baßler, J., & Dunin-Horkawicz, S. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-49674-0_4 · Cited by 116 · see citing works
Takahashi, A., Hayashi, N., Miyao, A., & Hirochika, H. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-175 · Cited by 116 · see citing works
Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome*
Wang, X., Cimermancic, P., Yu, C., Schweitzer, A., Chopra, N., Engel, J., Greenberg, C. H., Huszagh, A., Beck, F., Sakata, E., et al. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.065326 · Cited by 104 · see citing works
X-ray Crystal Structure Of A Trpm Assembly Domain Reveals An Antiparallel Four-stranded Coiled-coil
Fujiwara, Y., & Minor, D. L. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.12.2923 · Cited by 109 · see citing works
Integrating ELF4 into the circadian system through combined structural and functional studies
Kolmos, E., Nowak, M., Werner, M., Fischer-Schrader, K., Schwarz, G., Mathews, S., Schoof, H., Nagy, F., Bujnicki, J. M., & Davis, S. J. (2009) · HFSP journal · doi:10.2976/1.3218766 · Cited by 108 · see citing works
Sathyanarayana, B. K., Hahn, Y., Patankar, M. S., Pastan, I. H., & Lee, B. (2009) · BMC Structural Biology · doi:10.1186/1472-6807-9-1 · Cited by 104 · see citing works
Chen, J., Zheng, C., Ma, J., Jiang, C., Erċışlı, S., Yao, M.-Z., & Chen, L. (2020) · Horticulture Research · doi:10.1038/s41438-020-0288-2 · Cited by 104 · see citing works
Gordon, J., Hwang, J., Carrier, K., Jones, C. A., Kern, Q. L., Moreno, C. S., Karas, R. H., & Pallas, D. C. (2011) · BMC Biochemistry · doi:10.1186/1471-2091-12-54 · Cited by 101 · see citing works
Disentangling the complexity of low complexity proteins
Mier, P., Paladin, L., Tamana, S., Petrosian, S., Hajdu-Soltész, B., Urbanek, A., Gruca, A., Plewczyński, D., Grynberg, M., Bernadó, P., et al. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz007 · Cited by 97 · see citing works
The evolution and structure prediction of coiled coils across all genomes.
Rackham, O. J. L., Madera, M., Armstrong, C. T., Vincent, T. L., Woolfson, D. N., & Gough, J. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.032 · Cited by 97 · see citing works
Trigg, J., Gutwin, K., Keating, A. E., & Berger, B. (2011) · PLoS One · doi:10.1371/journal.pone.0023519 · Cited by 91 · see citing works
“Multicoil is based on the Paircoil algorithm [8,9], which uses a probabilistic framework to detect coiled-coil-forming segments in proteins, based on residue-pair frequencies in known coiled coils.”
MethodInfluentialSelf-citationThe molecular architecture of the nuclear basket
(2024) · doi:10.1016/j.cell.2024.07.020 · Cited by 94 · see citing works
Simm, D., Hatje, K., & Kollmar, M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu700 · Cited by 93 · see citing works
The Transposable Element Landscape of the Model LegumeLotus japonicus
Nagel, D. H., Zhang, X., Jiang, N., Pritham, E. J., & Wessler, S. R. (2006) · Genetics · doi:10.1534/genetics.106.062752 · Cited by 90 · see citing works
Shen, X., Salichos, L., & Rokas, A. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw179 · Cited by 91 · see citing works
Bogema, D. R., Deutscher, A. T., Woolley, L. K., Seymour, L. M., Raymond, B. B. A., Tacchi, J. L., Padula, M. P., Dixon, N. E., Minion, F. C., Jenkins, C., et al. (2012) · mBio · doi:10.1128/mbio.00282-11 · Cited by 88 · see citing works
Hariharan, V., & Hancock, W. O. (2009) · Cellular and Molecular Bioengineering · doi:10.1007/s12195-009-0059-5 · Cited by 82 · see citing works
Recruitment of two dyneins to an mRNA-dependent Bicaudal D transport complex
Sladewski, T. E., Billington, N., Ali, M. Y., Bookwalter, C. S., Lu, H., Krementsova, E. B., Schroer, T. A., & Trybus, K. M. (2018) · eLife · doi:10.7554/elife.36306 · Cited by 84 · see citing works
A new family of bacterial condensins
Petrushenko, Z. M., She, W., & Rybenkov, V. V. (2011) · Molecular Microbiology · doi:10.1111/j.1365-2958.2011.07763.x · Cited by 83 · see citing works
Coiled-coil networking shapes cell molecular machinery
Wang, Y., Zhang, X., Zhang, H., Lu, Y., Huang, H., Dong, X., Chen, J., Dong, J., Yang, X., Hang, H., et al. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e12-05-0396 · Cited by 83 · see citing works
Self-citationDeficiency of the E3 ubiquitin ligase TRIM2 in early-onset axonal neuropathy
Ylikallio, E., Pöyhönen, R., Zimoń, M., Vriendt, E. D., Hilander, T., Paetau, A. E., Jordanova, A., Lönnqvist, T. R. I., & Tyynismaa, H. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt149 · Cited by 82 · see citing works
Chen, X., Li, S., Zhang, D., Han, M., Jin, X., Zhao, C., Wang, S., Xing, L., Ma, J., Ji, J., et al. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400245 · Cited by 80 · see citing works
Gle1 Functions during mRNA Export in an Oligomeric Complex that Is Altered in Human Disease
Folkmann, A. W., Collier, S. E., Zhan, X., Aditi, A., Ohi, M. D., & Wente, S. R. (2013) · Cell · doi:10.1016/j.cell.2013.09.023 · Cited by 81 · see citing works
Mercier, A., & Labbé, S. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.009563 · Cited by 74 · see citing works
Purcell, E. B., McDonald, C. A., Palfey, B. A., & Crosson, S. (2010) · Biochemistry · doi:10.1021/bi1006404 · Cited by 73 · see citing works
Nibert, M. L., & Duncan, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068607 · Cited by 73 · see citing works
Frye, J. J., Klenchin, V. A., & Rayment, I. (2010) · Biochemistry · doi:10.1021/bi100349a · Cited by 72 · see citing works
Charged single α‐helix: A versatile protein structural motif
Süveges, D., Gáspári, Z., Tóth, G. J., & Nyitray, L. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22183 · Cited by 72 · see citing works
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
Li, A., Ai, L., Du, X., Chen, J.-Y., Yin, M., Hu, H., Shrestha, N., Wu, S., Wang, H., Dou, Q., et al. (2020) · Horticulture Research · doi:10.1038/s41438-020-00417-7 · Cited by 71 · see citing works
Pelassa, I., Corà, D., Cesano, F., Monje, F. J., Montarolo, P., & Fiumara, F. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu049 · Cited by 69 · see citing works
List, C., Qi, W., Maag, E., Gottstein, B., Müller, N., & Felger, I. (2010) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0000771 · Cited by 70 · see citing works
COMPUTATIONAL APPROACHES FOR RATIONAL DESIGN OF PROTEINS WITH NOVEL FUNCTIONALITIES
Tiwari, M. K., Singh, R., Singh, R. K., Kim, I., & Lee, J.-K. (2012) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201209002 · Cited by 69 · see citing works
Wu, W., Yang, Y., He, W., Rouard, M., Li, W.-M., Xu, M., Roux, N., & Ge, X. (2016) · Scientific Reports · doi:10.1038/srep31586 · Cited by 69 · see citing works
Chen, J., Peng, P., Tian, J., He, Y., Zhang, L., Liu, Z., Yin, D., & Zhang, Z. (2015) · Molecular Breeding · doi:10.1007/s11032-015-0305-6 · Cited by 68 · see citing works
Structure and Mechanical Properties of Human Trichocyte Keratin Intermediate Filament Protein
Chou, C., & Buehler, M. J. (2012) · Biomacromolecules · doi:10.1021/bm301254u · Cited by 68 · see citing works
Identification of novel synaptonemal complex components in C. elegans
Hurlock, M. E., Čavka, I., Kursel, L. E., Haversat, J., Wooten, M., Nizami, Z. F., Turniansky, R., Hoess, P., Ries, J., Gall, J. G., et al. (2020) · The Journal of Cell Biology · doi:10.1083/jcb.201910043 · Cited by 67 · see citing works
Genome-Wide Architecture of Disease Resistance Genes in Lettuce
Christopoulou, M., Reyes-Chin-Wo, S., Kozik, A., McHale, L. K., Truco, M. J., Wróblewski, T., & Michelmore, R. W. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.020818 · Cited by 66 · see citing works
Sharma, A. K., Mühlroth, A., Jouhet, J., Maréchal, É., Alipanah, L., Kissen, R., Brembu, T., Bones, A. M., & Winge, P. (2019) · New Phytologist · doi:10.1111/nph.16248 · Cited by 66 · see citing works
Multistate Organization of Transmembrane Helical Protein Dimers Governed by the Host Membrane
Polyansky, A. A., Volynsky, P. E., & Efremov, R. G. (2012) · Journal of the American Chemical Society · doi:10.1021/ja303483k · Cited by 65 · see citing works
Structures of Dimeric GIT1 and Trimeric β-PIX and Implications for GIT–PIX Complex Assembly
Schlenker, O., & Rittinger, K. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.050 · Cited by 65 · see citing works
Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint
Jackman, M. R., Marcozzi, C., Barbiero, M., Pardo, M., Yu, L., Tyson, A. L., Choudhary, J. S., & Pines, J. (2020) · The Journal of Cell Biology · doi:10.1083/jcb.201907082 · Cited by 62 · see citing works
Origin and Evolution of Laminin Gene Family Diversity
Fahey, B., & Degnan, B. M. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss060 · Cited by 61 · see citing works
The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots
Christie, N., Tobias, P. A., Naidoo, S., & Külheim, C. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2015.01238 · Cited by 61 · see citing works
Dorobantu, C. M., Albulescu, L., Lyoo, H., van Kampen, M., Francesco, R. D., Lohmann, V., Harak, C., van der Schaar, H. M., Strating, J. R. P. M., Gorbalenya, A. E., et al. (2016) · mSphere · doi:10.1128/msphere.00068-16 · Cited by 60 · see citing works
Hu, L. T., Xu, J., Xie, X., Zhou, Y., Tao, P., Li, H., Han, X., Wang, C., Liu, J., Xu, P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01290-0 · Cited by 60 · see citing works
Deutscher, A. T., Tacchi, J. L., Minion, F. C., Padula, M. P., Crossett, B., Bogema, D. R., Jenkins, C., Kuit, T. A., Walker, M. J., & Djordjevic, S. P. (2012) · Journal of Proteome Research · doi:10.1021/pr201115v · Cited by 59 · see citing works
Batzenschlager, M., Masoud, K., Janski, N., Houlné, G., Herzog, E., Evrard, J., Baumberger, N., Erhardt, M., Nominé, Y., Kieffer, B., et al. (2013) · Frontiers in Plant Science · doi:10.3389/fpls.2013.00480 · Cited by 58 · see citing works
McMichael, C. M., Reynolds, G. D., Koch, L. M., Wang, C., Jiang, N., Nadeau, J. A., Sack, F. D., Gelderman, M. B., Pan, J., & Bednarek, S. Y. (2013) · The Plant Cell · doi:10.1105/tpc.113.115162 · Cited by 58 · see citing works
Kunitake, E., Tani, S., Sumitani, J., & Kawaguchi, T. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4305-8 · Cited by 57 · see citing works
- Authors
- McDonnell, A. V., Jiang, T., Keating, A. E., & Berger, B.
- Affiliations
- MIT Computer Science and Artificial Intelligence Laboratory (US)
- Massachusetts Institute of Technology (US)
- Corresponding author
- Keating, A. E.
- Berger, B.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-11-29
- Volume
- 22
- Issue
- 3
- Pages
- 356-358
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2117709367
- Semantic Scholar
- 67080275c2f525632c88cf8bec8612acc6963372
- Cited by
- 424
- References
- 22
- Citations by year
- 2026: 5 · 2025: 8 · 2024: 16 · 2023: 15 · 2022: 18 · 2021: 27 · 2020: 19 · 2019: 25 · 2018: 19 · 2017: 27 · 2016: 25 · 2015: 22 · 2014: 25 · 2013: 22 · 2012: 41
- FWCI
- 4.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0347203, CAREER)
- National Institutes of Health
- National Institute of General Medical Sciences (GM67681, R01GM067681)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- coiled-coil domain, protein sequence analysis, web application, structure prediction
- MeSH terms
- Algorithms, Amino Acid Sequence, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Sensitivity and Specificity, Software, Reproducibility of Results, Sequence Analysis, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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