The DOI matches its Crossref record.
A standard reference frame for the description of nucleic acid base-pair geometry
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
No references could be resolved yet.
Research works printed but not linked: 37
- Lu, 1999, Resolving the discrepancies among nucleic acid conformation analyses, J. Mol. Biol., 285, 1563, 10.1006/jmbi.1998.2390 · DOI
- Dickerson, 1989, Definitions and nomenclature of nucleic acid structure parameters, EMBO J., 8, 1, 10.1002/j.1460-2075.1989.tb03339.x · DOI · Paper page
- Allen, 1979, The Cambridge Crystallographic Data Centre, Acta Crystallog. sect. B, 35, 2331, 10.1107/S0567740879009249 · DOI · Paper page
- Berman, 1992, The Nucleic Acid Database - a comprehensive relational database of three-dimensional structures of nucleic acids, Biophys. J., 63, 751, 10.1016/S0006-3495(92)81649-1 · DOI · Paper page
- Clowney, 1996, Geometric parameters in nucleic acids, J. Am. Chem. Soc., 118, 509, 10.1021/ja952883d · DOI
- Fujita, 1985, Model for interactions of amino acid side-chains with Watson-Crick base-pair of guanine and cytosine, Biochemistry, 24, 508, 10.1021/bi00323a039 · DOI
- Fujita, 1984, A model for interactions of amino acid side-chains with Watson-Crick base-pair of guanine and cytosine. Crystal structure of 9-(2-carboxyethyl)guanine and its crystalline complex with 1-methylcytosine, Bull. Chem. Soc. Jpn., 57, 1707, 10.1246/bcsj.57.1707 · DOI
- Wilson, 1988, Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases, Nucl. Acids Res., 16, 385, 10.1093/nar/16.2.385 · DOI
- Pirard, 1995, A database study of intermolecular NH…O hydrogen bonds for carboxylates, sulfonates, and monohydrogen phosphonates, Acta Crystallog. sect. B, 51, 103, 10.1107/S0108768194010566 · DOI
- Llamas-Saiz, 1990, N-H…N sp2 hydrogen interactions in organic crystals, J. Mol. Struct., 238, 367, 10.1016/0022-2860(90)85028-H · DOI
- Gavezzotti, 1994, Geometry of the intermolecular X-H…Y (X, Y = N,O) hydrogen bond and the calibration of empirical hydrogen-bond potentials, J. Phys. Chem., 98, 4831, 10.1021/j100069a010 · DOI
- Kim, 1993, Crystal structure of a yeast TBP/TATA-box complex, Nature, 365, 512, 10.1038/365512a0 · DOI · Paper page
- El Hassan, 1995, The assessment of the geometry of dinucleotide steps in double-helical DNA, J. Mol. Biol., 251, 648, 10.1006/jmbi.1995.0462 · DOI
- Lu, 1997, Structure and conformation of helical nucleic acids, J. Mol. Biol., 273, 668, 10.1006/jmbi.1997.1346 · DOI
- Gorin, 1995, B-DNA twisting correlates with base-pair morphology, J. Mol. Biol., 247, 34, 10.1006/jmbi.1994.0120 · DOI
- Kosikov, 1999, DNA stretching and compression, J. Mol. Biol., 289, 1301, 10.1006/jmbi.1999.2798 · DOI
- Lavery, 1988, The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids, J. Biomol. Struct. Dynam., 6, 63, 10.1080/07391102.1988.10506483 · DOI · Paper page
- Lavery, 1989, Defining the structure of irregular nucleic acids, J. Biomol. Struct. Dynam., 6, 655, 10.1080/07391102.1989.10507728 · DOI · Paper page
- Dickerson, 1998, DNA bending, Nucl. Acids Res., 26, 1906, 10.1093/nar/26.8.1906 · DOI · Paper page
- Soumpasis, 1988, A rigorous basepair oriented description of DNA structures, J. Biomol. Struct. Dynam., 6, 397, 10.1080/07391102.1988.10506497 · DOI
- Tung, 1994, An extension of the rigorous base-unit oriented description of nucleic acid structures, J. Biomol. Struct. Dynam., 11, 1327, 10.1080/07391102.1994.10508071 · DOI
- Bhattacharyya, 1989, A self- consistent formulation for analysis and generation of non-uniform DNA structures, J. Biomol. Struct. Dynam., 6, 635, 10.1080/07391102.1989.10507727 · DOI
- Bansal, 1995, NUPARM and NUCGEN, CABIOS, 11, 281
- Babcock, 1993, Nucleic acid structure analysis, J. Biomol. Struct. Dynam., 11, 597, 10.1080/07391102.1993.10508018 · DOI
- Babcock, 1994, Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures, J. Mol. Biol., 237, 125, 10.1006/jmbi.1994.1213 · DOI
- Babcock, 1994, The effect of mathematics and coordinate system on comparability and “dependencies” of nucleic acid structure parameters, J. Mol. Biol., 237, 98, 10.1006/jmbi.1994.1212 · DOI
- Schneider, 1997, Conformations of the sugar-phosphate backbone in helical DNA crystal structures, Biopolymers, 42, 113, 10.1002/(SICI)1097-0282(199707)42:1<113::AID-BIP10>3.0.CO;2-O · DOI
- Olson, 1993, Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA, J. Mol. Biol., 232, 530, 10.1006/jmbi.1993.1409 · DOI
- Olson, 1998, DNA sequence-dependent deformability deduced from protein-DNA crystal complexes, Proc. Natl Acad. Sci. USA, 95, 11163, 10.1073/pnas.95.19.11163 · DOI · Paper page
- Drew, 1981, Structure of a B-DNA dodecamer, Proc. Natl Acad. Sci. USA, 78, 2179, 10.1073/pnas.78.4.2179 · DOI · Paper page
- Calladine, 1984, A base- centered explanation of the B to A transition in DNA, J. Mol. Biol., 178, 773, 10.1016/0022-2836(84)90251-1 · DOI
- Fratini, 1982, Reversible bending and helix geometry in a B-DNA dodecamer, J. Biol. Chem., 257, 14686, 10.1016/S0021-9258(18)33335-0 · DOI · Paper page
- Lu, 1999, Mathematical overview of nucleic acid analysis programs, J. Biomol. Struct. Dynam., 16, 833, 10.1080/07391102.1999.10508296 · DOI
- Yanagi, 1991, Analysis of local helix geometry in three B-DNA decamers and eight dodecamers, J. Mol. Biol., 217, 201, 10.1016/0022-2836(91)90620-L · DOI
- Privé, 1991, Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G, J. Mol. Biol., 217, 177, 10.1016/0022-2836(91)90619-H · DOI · Paper page
- Hunter, 1987, The structure of guanosine-thymidine mismatches in B-DNA at 2.5 Å resolution, J. Biol. Chem., 262, 9962, 10.1016/S0021-9258(18)61060-9 · DOI
- Masquida, 2000, On the wobble G·U and related pairs, RNA, 6, 9, 10.1017/S1355838200992082 · DOI
Cited by
Martini coarse-grained force field: Extension to RNA
Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.05.043 · Cited by 259
The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation
Yeaton, A., Cayanan, G., Loghavi, S., Dolgalev, I., Leddin, E. M., Loo, C. E., Torabifard, H., Nicolet, D., Wang, J., Corrigan, K., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1146 · Cited by 94
Structural insights into the effects of 2’-5’ linkages on the RNA duplex
Sheng, J., Li, L., Engelhart, A. E., Gan, J., Wang, J., & Szostak, J. W. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317799111 · Cited by 50
On the Structure and Dynamics of Duplex GNA
Johnson, A. T., Schlegel, M. K., Meggers, E., Essen, L.-O., & Wiest, O. (2011) · The Journal of Organic Chemistry · doi:10.1021/jo201469b · Cited by 28
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
Metadata
- Authors
- Olson, W. K., Bansal, M., Burley, S. K., Dickerson, R. E., Gerstein, M., Harvey, S. C., Heinemann, U., Lu, X.-J., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C.-S., Westhof, E., Wolberger, C., & Berman, H. M.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2001-10
- Volume
- 313
- Issue
- 1
- Pages
- 229-237
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2100380699
- Cited by
- 597
- References
- 0
- FWCI
- 4.13
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- Funders
- Japan Science and Technology Corporation
- Japan Science and Technology Agency
- Core Research for Evolutional Science and Technology
- National Science Foundation (BIR 95 10703)
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A standard reference frame for the description of nucleic acid base-pair geometry. https://app.cochat.ai/papers/10.1006/jmbi.2001.4987
- The paper
- Olson, W. K., Bansal, M., Burley, S. K., Dickerson, R. E., Gerstein, M., Harvey, S. C., Heinemann, U., Lu, X.-J., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C.-S., Westhof, E., Wolberger, C., & Berman, H. M. (2001). A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology. https://doi.org/10.1006/jmbi.2001.4987
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.