AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
Abstract
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.
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The quality of Cn-AMP1 structures was evaluated by analyzing the Ramachandran diagram from PROCHECK-NMR.
“Furthermore, the quality of Cn-AMP1 structures was evaluated by analyzing the Ramachandran diagram that is part of the PROCHECK-NMR software [18,25].”
From Structural insights into <i>Cn</i>‐AMP1, a short disulfide‐free multifunctional peptide from green coconut water (2015) · cites this paper as [18]
The Ramachandran statistics among the top 20 lowest-energy structures are 98% for most favoured regions, 2% for additional allowed regions and 0% for disallowed regions.
“On the basis of Procheck82 analysis of secondary structure elements, the Ramachandran statistics among the top 20 lowest-energy structures are 98% for most favoured regions, 2% for additional allowed regions and 0% for disallowed regions.”
From Predicting multiple conformations via sequence clustering and AlphaFold2 (2024) · cites this paper as [82]
Cites
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581 · see citing works
Self-citationKabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,582 · see citing works
MOLMOL: A program for display and analysis of macromolecular structures
Koradi, R., Billeter, M., & Kurt Wüthrich, A. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00009-4 · Cited by 7,163 · see citing works
Stereochemistry of polypeptide chain configurations
Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963) · Journal of Molecular Biology · doi:10.1016/s0022-2836(63)80023-6 · Cited by 3,549 · see citing works
X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
Brünger, A. T. (1992) · Medical Entomology and Zoology · Cited by 3,439 · see citing works
Stereochemical quality of protein structure coordinates
Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340120407 · Cited by 1,547 · see citing works
Self-citationGüntert, P., Braun, W. A., & Kurt Wüthrich, A. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90754-t · Cited by 784 · see citing works
Havel, T. F. (1991) · Progress in Biophysics and Molecular Biology · doi:10.1016/0079-6107(91)90007-f · Cited by 425 · see citing works
PostScript Language Reference Manual
Press, A. (1985) · Addison-Wesley Longman Publishing Co., Inc. eBooks · Cited by 317 · see citing works
Havel, T. F., & Wüthrich, K. (1984) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(84)80066-x · Cited by 288 · see citing works
NMR of macromolecules : a practical approach
Roberts, G. C. K. (1993) · Oxford University Press eBooks · Cited by 225 · see citing works
Calvert, P. (1977) · Nature · doi:10.1038/268105a0 · Cited by 156 · see citing works
Clore, G. M., Robien, M. A., & Gronenborn, A. M. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1259 · Cited by 155 · see citing works
Thomas, P. D., Basus, V. J., & James, T. L. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.4.1237 · Cited by 138 · see citing works
Solution Structure of the HU Protein fromBacillus stearothermophilus
Vis, H., Mariani, M., Vorgias, C. E., Wilson, K. S., Kaptein, R., & Boelens, R. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0648 · Cited by 100 · see citing works
Self-citationHoch, J. C., Poulsen, F. M., & Redfield, C. (1991) · Springer eBooks · doi:10.1007/978-1-4757-9794-7 · Cited by 91 · see citing works
González, C., Rullmann, J. A. C., Bonvin, A. M. J. J., Boelens, R., & Kaptein, R. (1991) · Journal of Magnetic Resonance (1969) · doi:10.1016/0022-2364(91)90397-c · Cited by 84 · see citing works
Self-citationAn Assessment of the Precision and Accuracy of Protein Structures Determined by NMR
Zhao, D., & Jardetzky, O. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1402 · Cited by 77 · see citing works
Conformational analysis of protein structures derived from NMR data
MacArthur, M. W., & Thornton, J. M. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170303 · Cited by 64 · see citing works
Self-citationNMR structures and methodology
Chazin, W. (1992) · Current Opinion in Biotechnology · doi:10.1016/0958-1669(92)90159-g · Cited by 5 · see citing works
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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Comparative Protein Structure Modeling Using Modeller
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s15 · Cited by 4,564 · see citing works
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Davis, I., Leaver‐Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J. S., Richardson, J. S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm216 · Cited by 3,915 · see citing works
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169 · see citing works
Comparative Protein Structure Modeling Using MODELLER
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2007) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0209s50 · Cited by 2,862 · see citing works
Structure and ligand of a histone acetyltransferase bromodomain
Dhalluin, C., Carlson, J. E., Zeng, L., He, C., Aggarwal, A. K., Zhou, M.-M., & Zhou, M.-M. (1999) · Nature · doi:10.1038/20974 · Cited by 1,732 · see citing works
Yap, K. L., Li, S., Muñoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., Gil, J., Walsh, M. J., & Zhou, M.-M. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.021 · Cited by 1,391 · see citing works
The Process of Structure-Based Drug Design
Anderson, A. C. (2003) · Chemistry & Biology · doi:10.1016/j.chembiol.2003.09.002 · Cited by 943 · see citing works
Elfiky, A. A. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.117592 · Cited by 929 · see citing works
Structural mechanism of plant aquaporin gating
Törnroth‐Horsefield, S., Wang, Y., Hedfalk, K., Johanson, U., Karlsson, M. E., Tajkhorshid, E., Neutze, R., & Kjellbom, P. O. (2005) · Nature · doi:10.1038/nature04316 · Cited by 863 · see citing works
Consistent blind protein structure generation from NMR chemical shift data
Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J. M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K. K., Lemak, A., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800256105 · Cited by 855 · see citing works
Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M. M., Nussinov, R., & Ishii, Y. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2991 · Cited by 822 · see citing works
Craik, D. J., Daly, N. L., Bond, T., & Waine, C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3383 · Cited by 810 · see citing works
Autoinhibition and activation mechanisms of the Wiskott–Aldrich syndrome protein
Kim, A. S., Kakalis, L. T., Abdul-Manan, N., Liu, G. A., & Rosen, M. K. (2000) · Nature · doi:10.1038/35004513 · Cited by 752 · see citing works
Structural basis for the recognition of hydroxyproline in HIF-1α by pVHL
Hon, W.-C., Wilson, M. I., Harlos, K., Claridge, T. D. W., Schofield, C. J., Pugh, C. W., Maxwell, P. H., Ratcliffe, P. J., Stuart, D. I., & Jones, E. Y. (2002) · Nature · doi:10.1038/nature00767 · Cited by 751 · see citing works
Evaluating protein structures determined by structural genomics consortia
Bhattacharya, A., Tejero, R., & Montelione, G. T. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21165 · Cited by 729 · see citing works
Radhakrishnan, I., Pérez-Alvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., & Wright, P. E. (1997) · Cell · doi:10.1016/s0092-8674(00)80463-8 · Cited by 728 · see citing works
Anti-HCV, nucleotide inhibitors, repurposing against COVID-19
Elfiky, A. A. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.117477 · Cited by 719 · see citing works
SHIFTX2: significantly improved protein chemical shift prediction
Han, B., Liu, Y., Ginzinger, S., & Wishart, D. S. (2011) · Journal of Biomolecular NMR · doi:10.1007/s10858-011-9478-4 · Cited by 673 · see citing works
Structural Basis of Integrin Activation by Talin
Wegener, K. L., Partridge, A. W., Han, J., Pickford, A. R., Liddington, R., Ginsberg, M. H., & Campbell, I. D. (2007) · Cell · doi:10.1016/j.cell.2006.10.048 · Cited by 677 · see citing works
Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus
Mygind, P. H., Fischer, R. L., Schnorr, K. M., Hansen, M. T., Sönksen, C. P., Ludvigsen, S., Raventós, D., Buskov, S., Christensen, B. B., Maria, L. D., et al. (2005) · Nature · doi:10.1038/nature04051 · Cited by 655 · see citing works
Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain
Liu, Z., Sun, C. C., Olejniczak, E. T., Meadows, R. P., Betz, S. F., Oost, T. K., Herrmann, J. E., Wu, J. C., & Fesik, S. W. (2000) · Nature · doi:10.1038/35050006 · Cited by 647 · see citing works
Open channel structure of MscL and the gating mechanism of mechanosensitive channels
Perozo, E., Cortés, D. M., Sompornpisut, P., Kloda, A., & Martinac, B. (2002) · Nature · doi:10.1038/nature00992 · Cited by 616 · see citing works
Predicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545 · see citing works
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
Neal, S., Nip, A. M., Zhang, H., & Wishart, D. S. (2003) · Journal of Biomolecular NMR · doi:10.1023/a:1023812930288 · Cited by 540 · see citing works
Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination
Tang, J., Cho, N. W., Cui, G., Manion, E. M., Shanbhag, N. M., Botuyan, M. V., Mer, G., & Greenberg, R. A. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2499 · Cited by 521 · see citing works
Kortemme, T., Morozov, A. V., & Baker, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00021-4 · Cited by 519 · see citing works
Hagn, F., Etzkorn, M., Raschle, T., & Wagner, G. (2013) · Journal of the American Chemical Society · doi:10.1021/ja310901f · Cited by 499 · see citing works
Structure of a BRCA1-BARD1 heterodimeric RING-RING complex.
Brzović, P. S., Rajagopal, P., Hoyt, D. W., King, M., & Klevit, R. E. (2001) · Nature Structural Biology · doi:10.1038/nsb1001-833 · Cited by 494 · see citing works
Allen, M. D., Yamasaki, K., Ohme‐Takagi, M., Tateno, M., & Suzuki, M. (1998) · The EMBO Journal · doi:10.1093/emboj/17.18.5484 · Cited by 490 · see citing works
Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor
Endres, N., Das, R., Smith, A. W., Arkhipov, A. S., Kovács, E., Huang, Y., Pelton, J. G., Shan, Y., Shaw, D. E., Wemmer, D. E., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.032 · Cited by 493 · see citing works
Shi, J., Wang, Y., Zeng, L., Wu, Y., Deng, J., Zhang, Q., Lin, Y., Li, J., Kang, T., Tao, M., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.01.028 · Cited by 483 · see citing works
Wang, G. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m805533200 · Cited by 483 · see citing works
Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut
Fung, T. C., Vuong, H. E., Luna, C. G. G., Pronovost, G. N., Aleksandrova, A. A., Riley, N. G., Vavilina, A., McGinn, J., Rendon, T. K., Forrest, L. R., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0540-4 · Cited by 481 · see citing works
Nonself RNA-Sensing Mechanism of RIG-I Helicase and Activation of Antiviral Immune Responses
Takahasi, K., Yoneyama, M., Nishihori, T., Hirai, R., Kumeta, H., Narita, R., Gale, M., Inagaki, F., & Fujita, T. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.11.028 · Cited by 474 · see citing works
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E., & Kurt Wüthrich, A. (1998) · Journal of Biomolecular NMR · doi:10.1023/a:1008290618449 · Cited by 467 · see citing works
Self-citationStructural basis for recruitment of CBP/p300 by hypoxia-inducible factor-1α
Freedman, S. J., Sun, Z., Poy, F., Kung, A. L., Livingston, D. M., Wagner, G., & Eck, M. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082117899 · Cited by 457 · see citing works
Structure of the chemokine receptor CXCR1 in phospholipid bilayers
Park, S. H., Das, B. B., Casagrande, F., Tian, Y., Nothnagel, H. J., Chu, M., Kiefer, H., Maier, K., Angelis, A. A. D., Marassi, F. M., et al. (2012) · Nature · doi:10.1038/nature11580 · Cited by 459 · see citing works
Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators
Demarest, S. J., Martinez‐Yamout, M. A., Chung, J., Chen, H.-W., Xu, W., Dyson, H. J., Evans, R. M., & Wright, P. E. (2002) · Nature · doi:10.1038/415549a · Cited by 452 · see citing works
Transglutaminase 2 Undergoes a Large Conformational Change upon Activation
Pinkas, D. M., Strop, P., Brünger, A. T., & Khosla, C. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050327 · Cited by 452 · see citing works
Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain
Lingel, A., Simon, B., Izaurralde, E., & Sattler, M. (2003) · Nature · doi:10.1038/nature02123 · Cited by 451 · see citing works
Han, X., Bushweller, J. H., Cafiso, D. S., & Tamm, L. K. (2001) · Nature Structural Biology · doi:10.1038/90434 · Cited by 450 · see citing works
Structural insights into the degradation of Mcl-1 induced by BH3 domains
Czabotar, P. E., Lee, E. F., van Delft, M. F., Day, C. L., Smith, B. J., Huang, D. C. S., Fairlie, W. D., Hinds, M. G., & Colman, P. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701297104 · Cited by 449 · see citing works
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger
Wang, G. G., Song, J., Wang, Z., Dormann, H. L., Casadio, F., Li, H., Luo, J.-L., Patel, D. J., & Allis, C. D. (2009) · Nature · doi:10.1038/nature08036 · Cited by 439 · see citing works
Evolutionary information for specifying a protein fold
Socolich, M., Lockless, S. W., Russ, W. P., Lee, H. J., Gardner, K. H., & Ranganathan, R. (2005) · Nature · doi:10.1038/nature03991 · Cited by 437 · see citing works
Bateman, A., & Bycroft, M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3778 · Cited by 432 · see citing works
Structural Basis for Tumor Pyruvate Kinase M2 Allosteric Regulation and Catalysis ,
Dombrauckas, J. D., Santarsiero, B. D., & Mesecar, A. D. (2005) · Biochemistry · doi:10.1021/bi0474923 · Cited by 414 · see citing works
Petros, A. M., Nettesheim, D. G., Wang, Y., Olejniczak, E. T., Meadows, R. P., Mack, J. C., Swift, K. M., Matayoshi, E. D., Zhang, H., Thompson, C. B., et al. (2000) · Protein Science · doi:10.1110/ps.9.12.2528 · Cited by 413 · see citing works
Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43
Lukavsky, P. J., Daujotyte, D., Tollervey, J. R., Ule, J., Stuani, C., Buratti, E., Baralle, F. E., Damberger, F. F., & Allain, F. H. ‐. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2698 · Cited by 408 · see citing works
Structural basis for Hif-1α/CBP recognition in the cellular hypoxic response
Dames, S. A., Martinez‐Yamout, M. A., Guzman, R. N. D., Dyson, H. J., & Wright, P. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082121399 · Cited by 404 · see citing works
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E., & Kurt Wüthrich, A. (1998) · Pure and Applied Chemistry · doi:10.1351/pac199870010117 · Cited by 402 · see citing works
Self-citationStructure of an Intermediate State in Protein Folding and Aggregation
Neudecker, P., Robustelli, P., Cavalli, A., Walsh, P., Lundström, P., Zarrine‐Afsar, A., Sharpe, S. J., Vendruscolo, M., & Kay, L. E. (2012) · Science · doi:10.1126/science.1214203 · Cited by 399 · see citing works
Solution Structure of the Proapoptotic Molecule BID
McDonnell, J. M., Fushman, D., Milliman, C. L., Korsmeyer, S. J., & Cowburn, D. (1999) · Cell · doi:10.1016/s0092-8674(00)80573-5 · Cited by 396 · see citing works
Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.
Arora, A., Abildgaard, F., Bushweller, J. H., & Tamm, L. K. (2001) · Nature Structural Biology · doi:10.1038/86214 · Cited by 389 · see citing works
Aghazadeh, B., Lowry, W. E., Huang, X.-Y., & Rosen, M. K. (2000) · Cell · doi:10.1016/s0092-8674(00)00085-4 · Cited by 383 · see citing works
Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes
Thestrup, T., Litzlbauer, J., Bartholomäus, I., Mues, M., Russo, L., Dana, H., Kovalchuk, Y., Liang, Y., Kalamakis, G., Laukat, Y., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2773 · Cited by 366 · see citing works
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d
Hudson, B. P., Martinez‐Yamout, M. A., Dyson, H. J., & Wright, P. E. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb738 · Cited by 367 · see citing works
Shen, Y., & Bax, A. (2007) · Journal of Biomolecular NMR · doi:10.1007/s10858-007-9166-6 · Cited by 362 · see citing works
Mutations in a newly identified GTPase gene cause autosomal dominant hereditary spastic paraplegia
Zhao, X., Alvarado, D., Rainier, S., Lemons, R., Hedera, P., Weber, C. H., Tukel, T., Apak, M., Heiman-Patterson, T., Ming, L., et al. (2001) · Nature Genetics · doi:10.1038/ng758 · Cited by 357 · see citing works
Dormitzer, P. R., Sun, Z. J., Wagner, G., & Harrison, S. C. (2002) · The EMBO Journal · doi:10.1093/emboj/21.5.885 · Cited by 347 · see citing works
Four New Members Expand the Interleukin-1 Superfamily
Smith, D. E., Renshaw, B. R., Ketchem, R. R., Kubin, M. Z., Garka, K. E., & Sims, J. E. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.2.1169 · Cited by 341 · see citing works
Hsu, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki725 · Cited by 337 · see citing works
Structure and function of the complex formed by the tuberculosis virulence factors CFP‐10 and ESAT‐6
Renshaw, P. S., Lightbody, K. L., Veverka, V., Muskett, F. W., Kelly, G. P., Frenkiel, T. A., Gordon, S. V., Hewinson, R. G., Burke, B., Norman, J. C., et al. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600732 · Cited by 329 · see citing works
Solution structure and dynamics of the outer membrane enzyme PagP by NMR
Hwang, P. M., Choy, W., Lo, E. I., Chen, L., Forman-Kay, J. D., Raetz, C. R. H., Privé, G. G., Bishop, R. E., & Kay, L. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212344499 · Cited by 324 · see citing works
SMN tudor domain structure and its interaction with the Sm proteins.
Sattler, M., Selenko, P., Sprangers, R., Stier, G., Bühler, D., & Fischer, U. (2001) · Nature Structural Biology · doi:10.1038/83014 · Cited by 324 · see citing works
10 Residue Folded Peptide Designed by Segment Statistics
Honda, S., Yamasaki, K., Sawada, Y., & Morii, H. (2004) · Structure · doi:10.1016/j.str.2004.05.022 · Cited by 323 · see citing works
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b
Zeng, L., Zhang, Q., Li, S., Plotnikov, A. N., Walsh, M. J., & Zhou, M. (2010) · Nature · doi:10.1038/nature09139 · Cited by 321 · see citing works
Entropic switch regulates myristate exposure in the HIV-1 matrix protein
Tang, C., Loeliger, E., Luncsford, P. J., Kinde, I., Beckett, D., & Summers, M. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305665101 · Cited by 320 · see citing works
Structural Mechanism of the Bromodomain of the Coactivator CBP in p53 Transcriptional Activation
Mujtaba, S., He, Y., Zeng, L., Yan, S. X., Plotnikova, O. V., Sachchidanand, Sánchez, R., Zeleznik‐Le, N. J., Ronai, Z. A., & Zhou, M. (2004) · Molecular Cell · doi:10.1016/s1097-2765(03)00528-8 · Cited by 318 · see citing works
Abdul-Manan, N., Aghazadeh, B., Liu, G. A., Majumdar, A. K., Ouerfelli, O., Siminovitch, K., & Rosen, M. K. (1999) · Nature · doi:10.1038/20726 · Cited by 315 · see citing works
Cysteine-rich module structure reveals a fulcrum for integrin rearrangement upon activation
Beglova, N., Blacklow, S. C., Takagi, J., & Springer, T. A. (2002) · Nature Structural Biology · doi:10.1038/nsb779 · Cited by 314 · see citing works
Solution Structure of the Methyl-CpG Binding Domain of Human MBD1 in Complex with Methylated DNA
Ohki, I., Shimotake, N., Fujita, N., Jee, J.-G., Ikegami, T., Nakao, M., & Shirakawa, M. (2001) · Cell · doi:10.1016/s0092-8674(01)00324-5 · Cited by 313 · see citing works
Yamasaki, K., Kigawa, T., Inoue, M., Tateno, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Nunokawa, E., et al. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.01.015 · Cited by 310 · see citing works
Hosoda, K., Imamura, A., Katoh, E., Hatta, T., Tachiki, M., Yamada, H., Mizuno, T., & Yamazaki, T. (2002) · The Plant Cell · doi:10.1105/tpc.002733 · Cited by 310 · see citing works
The Protein Data Bank: unifying the archive
Westbrook, J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.245 · Cited by 309 · see citing works
Ilangovan, U., Ton-That, H., Iwahara, J., Schneewind, O., & Clubb, R. T. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.101064198 · Cited by 304 · see citing works
Chang, C.-I., Xu, B.-E., Akella, R., Cobb, M. H., & Goldsmith, E. J. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00525-7 · Cited by 302 · see citing works
Structure and Function of the Membrane Anchor Domain of Hepatitis C Virus Nonstructural Protein 5A
Pénin, F., Brass, V., Appel, N., Ramboarina, S., Montserret, R., Ficheux, D., Blum, H. E., Bartenschlager, R. F. W., & Moradpour, D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m404761200 · Cited by 301 · see citing works
Structure and functional interactions of the Tsg101 UEV domain
Pornillos, O., Alam, S. L., Rich, R. L., Myszka, D. G., Davis, D. R., & Sundquist, W. I. (2002) · The EMBO Journal · doi:10.1093/emboj/21.10.2397 · Cited by 301 · see citing works
Recommendations for the presentation of NMR structures of proteins and nucleic acids
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E., & Kurt Wüthrich, A. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1852 · Cited by 301 · see citing works
Self-citationA new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS
Wang, X., Lord, D. M., Cheng, H.-Y., Osbourne, D. O., Hong, S. H., Sánchez-Torres, V., Quiroga, C., Zheng, K., Herrmann, T., Peti, W., et al. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.1062 · Cited by 299 · see citing works
Structural insights into the U-box, a domain associated with multi-ubiquitination
Ohi, M. D., Kooi, C. W. V., Rosenberg, J. A., Chazin, W., & Gould, K. L. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb906 · Cited by 295 · see citing works
SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective
Elfiky, A. A. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1761882 · Cited by 284 · see citing works
Melckebeke, H. V., Wasmer, C., Lange, A., Eiso, A. B., Loquet, A., Böckmann, A., & Meier, B. H. (2010) · Journal of the American Chemical Society · doi:10.1021/ja104213j · Cited by 283 · see citing works
A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling
Divakar, S. K. A., Carpio, R. V., Dutta, K., Baker, S. J., Cosenza, S. C., Basu, I., Gupta, Y. K., Reddy, M. V. R., Ueno, L. A., Hart, J. R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.045 · Cited by 278 · see citing works
Solution Structure of the Transmembrane H+-Transporting Subunit c of the F1Fo ATP Synthase
Girvin, M. E., Rastogi, V. K., Abildgaard, F., Markley, J. L., & Fillingame, R. H. (1998) · Biochemistry · doi:10.1021/bi980511m · Cited by 278 · see citing works
Pell, L. G., Kanelis, V., Donaldson, L. W., Howell, P. L., & Davidson, A. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900044106 · Cited by 276 · see citing works
Jehle, S., Rajagopal, P., Bardiaux, B., Marković, S., Kühne, R., Stout, J. R., Higman, V. A., Klevit, R. E., van Rossum, B., & Oschkinat, H. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1891 · Cited by 276 · see citing works
Structure of the Alzheimer's Disease Amyloid Precursor Protein Copper Binding Domain
Barnham, K. J., McKinstry, W. J., Multhaup, G., Galatis, D., Morton, C. J., Curtain, C. C., Williamson, N. A., White, A. R., Hinds, M. G., Norton, R. S., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300629200 · Cited by 274 · see citing works
Das, K., Xiong, X., Yang, H., Westland, C. E., Gibbs, C. S., Sarafianos, S. G., & Arnold, E. (2001) · Journal of Virology · doi:10.1128/jvi.75.10.4771-4779.2001 · Cited by 274 · see citing works
NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1
Guettler, T., Madl, T., Neumann, P., Deichsel, D., Corsini, L., Monecke, T., Ficner, R., Sattler, M., & Görlich, D. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1931 · Cited by 271 · see citing works
A minimal sequence code for switching protein structure and function
Alexander, P., He, Y., Chen, Y., Orban, J. P., & Bryan, P. N. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906408106 · Cited by 270 · see citing works
Small Ubiquitin-like Modifier (SUMO) Recognition of a SUMO Binding Motif
Song, J., Zhang, Z., Hu, W., & Chen, Y. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m507059200 · Cited by 267 · see citing works
Molecular basis of RNA recognition by the human alternative splicing factor Fox-1
Auweter, S. D., Fasan, R., Reymond, L., Underwood, J. G., Black, D. L., Pitsch, S., & Allain, F. H. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600918 · Cited by 264 · see citing works
MIA40 is an oxidoreductase that catalyzes oxidative protein folding in mitochondria
Banci, L., Bertini, I., Cefaro, C., Ciofi‐Baffoni, S., Gallo, A., Martinelli, M., Sideris, D. P., Katrakili, N., & Tokatlidis, K. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1553 · Cited by 261 · see citing works
Structure of Adeno-Associated Virus Serotype 8, a Gene Therapy Vector
Nam, H.-J., Lane, M. D., Padron, E., Gurda, B. L., McKENNA, R. V., Kohlbrenner, E., Aslanidi, G., Byrne, B. J., Muzyczka, N., Zolotukhin, S., et al. (2007) · Journal of Virology · doi:10.1128/jvi.01304-07 · Cited by 256 · see citing works
Byeon, I.-J. L., Meng, X., Jung, J., Zhao, G., Yang, R., Ahn, J., Shi, J., Concel, J., Aiken, C., Zhang, P., et al. (2009) · Cell · doi:10.1016/j.cell.2009.10.010 · Cited by 253 · see citing works
Huang, Y. J., Powers, R., & Montelione, G. T. (2005) · Journal of the American Chemical Society · doi:10.1021/ja047109h · Cited by 253 · see citing works
Camenisch, G., Pisabarro, M. T., Sherman, D. A., Kowalski, J., Nagel, M., Hass, P., Xie, M.-H., Gurney, A. L., Bodary, S. C., Liang, X. H., et al. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109768200 · Cited by 253 · see citing works
Linge, J. P., & Nilges, M. (1999) · Journal of Biomolecular NMR · doi:10.1023/a:1008365802830 · Cited by 253 · see citing works
- Authors
- Laskowski, R., Rullmann, J. A., MacArthur, M., Kaptein, R., & Thornton, J.
- Affiliations
- Utrecht University (NL)
- ORCID
- Kaptein, Robert
- Venue
- Journal of Biomolecular NMR
- Published
- 1996-12
- Volume
- 8
- Issue
- 4
- Pages
- 477-86
- ISSN
- 0925-2738 (ISSN-L)
- 1573-5001
- OpenAlex
- W1975459052
- Cited by
- 5,502
- References
- 21
- Citations by year
- 2026: 142 · 2025: 203 · 2024: 205 · 2023: 219 · 2022: 238 · 2021: 204 · 2020: 198 · 2019: 153 · 2018: 130 · 2017: 173 · 2016: 191 · 2015: 194 · 2014: 248 · 2013: 248 · 2012: 233
- FWCI
- 21.02
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Biomolecular NMR (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- Aqua, protein conformational ensembles
- MeSH terms
- Amino Acid Sequence, Bacterial Proteins, DNA-Binding Proteins, Evaluation Studies as Topic, Models, Molecular, Molecular Sequence Data, Magnetic Resonance Spectroscopy, Proteins, Quality Control, Software, Solutions, Reproducibility of Results, Molecular Structure, Protein Structure, Secondary
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