A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

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 8,574

NMR of Proteins and Nucleic Acids

(2006) · Royal Society of Chemistry eBooks · doi:10.1039/9781847555236-00336 · Cited by 5,874

X-PLOR Version 3.1: A System for X-ray Crystallography and NMR

Brünger, A. T. (1992) · Medical Entomology and Zoology · Cited by 3,424

Conformation of Polypeptides and Proteins

Ramachandran, G. N., & Sasisekharan, V. (1968) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60402-7 · Cited by 2,953

Torsion angle dynamics for NMR structure calculation with the new program Dyana

Güntert, P., Mumenthaler, C., & Kurt Wüthrich, A. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1284 · Cited by 2,781

Protein NMR Structure Determination with Automated NOE Assignment Using the New Software CANDID and the Torsion Angle Dynamics Algorithm DYANA

Herrmann, T., Güntert, P., & Wüthrich, K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00241-3 · Cited by 1,472

Taschenbuch der Mathematik

Bronshtein, I. N., & Semendjaev, K. A. (1966) · CERN Document Server (European Organization for Nuclear Research) · Cited by 1,467

Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin 1 1Edited by P. E. Wright

Nilges, M., Macías, M. J., O’Donoghue, S. I., & Oschkinat, H. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1044 · Cited by 429

A relational database for sequence-specific protein NMR data

Seavey, B. R., Farr, E. A., Westler, W. M., & Markley, J. L. (1991) · Journal of Biomolecular NMR · doi:10.1007/bf01875516 · Cited by 353

Kooperation zwischen T‐Domäne und minimaler C‐terminaler Docking‐Domäne für funktionelle Proteininteraktionen in Multiprotein‐NRPS

Watzel, J., Duchardt, E., Sarawi, S., Bode, H. B., & Wöhnert, J. (2021) · Angewandte Chemie · doi:10.1002/ange.202103498 · Cited by 1

1H, 13C, 15N backbone and side-chain chemical shift assignments of the polyketide cyclase from Mycobacterium tuberculosis

Fan, S., Zhuang, J., Guo, C., Lin, D., & Liao, X. (2021) · Biomolecular NMR Assignments · doi:10.1007/s12104-021-10036-5 · Cited by 1

Innentitelbild: Gausemycins A,B: Cyclic Lipoglycopeptides from Streptomyces sp. (Angew. Chem. 34/2021)

Tyurin, A. P., Alferova, V. A., Paramonov, A. S., Shuvalov, M. V., Kudryakova, G. K., Rogozhin, E. A., Zherebker, A., Brylev, V. A., Chistov, A. A., Baranova, A. A., et al. (2021) · Angewandte Chemie · doi:10.1002/ange.202107693 · Cited by 1

The LEF-1 high-mobility group box adopts residual structure in its DNA-free form

Alderson, T. R., Habacher, H., Bourgeois, B. M. R., & Madl, T. (2022) · Journal of Magnetic Resonance Open · doi:10.1016/j.jmro.2022.100074 · Cited by 1

Site-Specific Structure and Dynamics of Polyglutamine-Containing Amyloid Fibrils and the Caveolin Scaffolding Domain by Magic Angle Spinning Solid-State NMR

Hoop, C. L. (2014) · D-Scholarship@Pitt (University of Pittsburgh)

1H, 13C, and 15N resonance assignments for the tandem PHD finger motifs of human CHD4

Walport, L. J., Morra, R., Mancini, E. J., & Redfield, C. (2014) · Biomolecular NMR Assignments · doi:10.1007/s12104-014-9582-y

NMR Spectroscopy of Multi-domain Proteins : Immunoglobulin-like Domains of Human Filamin A

Koskela, O. (2009) · Työväentutkimus Vuosikirja

of the phosphoesterase (PE) domain of Pseudomonas aeruginosa DNA ligase D (LigD)

Nair, A. (2011)

Solution structure of an archaeal DUF61 family protein SSO0941 encoded by a gene in the operon of box C/D RNA protein complexes

Zhou, T., Yao, X., Wang, J., & Feng, Y. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.03.003

РЕКОМБИНАНТНАЯ ПРОДУКЦИЯ И ИССЛЕДОВАНИЕ СТРУКТУРЫ БЕЛКОВ ЧЕЛОВЕКА LYPD6 И LYPD6B1, "Биоорганическая химия"

Парамонов, А. С., Kulbatskii, D. S., Loktyushov, E. V., Tsarev, A. V., Dolgikh, D. A., Shenkarev, Z. O., Кирпичников, М. П., & Люкманова, Е. Н. (2017) · Биоорганическая химия · doi:10.7868/s0132342317060045

1H, 13C, and 15N Backbone assignments of the human brain and acute leukemia cytoplasmic (BAALC) protein

Láng, A., Kumar, A., Jirschitzka, J., Bordusa, F., Ohlenschläger, O., & Wiedemann, C. (2020) · Biomolecular NMR Assignments · doi:10.1007/s12104-020-09938-7

Comment on mr-2021-37

Felli, I. C. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-37-ac1

Comment on mr-2021-54

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-rc2

Comment on mr-2021-54

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-rc1

Selective1HαNMR Methods Reveal Functionally Relevant Prolinecis/transIsomers in Intrinsically Disordered Proteins: Characterization of Minor Forms, Effects of Phosphorylation, and Occurrence in Proteome

Sebák, F., Ecsédi, P., Bermel, W., Luy, B., Nyitray, L., & Bodor, A. (2021) · Angewandte Chemie · doi:10.1002/ange.202108361

Comment on mr-2021-54

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-rc3

Comment on mr-2021-37

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-37-rc1

Comment on mr-2021-37

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-37-rc2

References

(2012) · Wiley eBooks · doi:10.1002/9783527644506.refs

Reply on RC1

Kieffer, B. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-ac1

Reply on RC2

Kieffer, B. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-ac2

Reply on RC3

Kieffer, B. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-54-ac3

Insight into Polyproline II Helical Bundle Stability and Folding from NMR Spectroscopic Characterization of the Snow Flea Antifreeze Protein Denatured StatePreprint

Treviño, M. Á., Moya, M. R., Sánchez, R. L., Pantoja‐Uceda, D., Mompeán, M., & Laurents, D. V. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.10.483783

Peptide Toxin Structure and Function by NMR

Norton, R. S. (2017) · Springer eBooks · doi:10.1007/978-3-319-28275-6_120-1

Backbone and side chain NMR assignment of the heme-nitric oxide/oxygen binding (H-NOX) domain from Nostoc punctiforme

Chasapi, S. A., Argyriou, A. I., & Spyroulias, G. A. (2022) · Biomolecular NMR Assignments · doi:10.1007/s12104-022-10107-1

Making the Most of Chemical Shifts

Broadhurst, R. W. (2012) · Royal Society of Chemistry eBooks · doi:10.1039/9781849731201-00053

Structural analysis of an Asterias rubens peptide indicates the presence of a disulfide‐directed β‐hairpin fold

Takjoo, R., Wilson, D. T. R., Quilliec, J. L., Schmidt, C. A., Zhao, G., Liddell, M. J., Shaikh, N., Sunagar, K., Loukas, A. C., Smout, M. J., et al. (2024) · FEBS Open Bio · doi:10.1002/2211-5463.13931 · Cited by 1

Functional studies and molecular dynamics reveal BPP-BrachyNH2-induced relaxation in male rat small mesenteric arteries via binding to argininosuccinate synthase

Arcanjo, D. D. R., Bezerra, I. B. M., Comerma-Steffensen, S., Prat‐Duran, J., Moreira, D. C., Vasconcelos, A. G., Plácido, A., Teixeira, C. A. S., Gomes, P. A. C., Cardoso‐Teixeira, A. C., et al. (2025) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2025.177857

Solution structure of the C-terminal domain of the measles virus V protein in its free form and mechanistic analysis of STAT2 targeting

Morita, K., Goda, N., Kimoto, M., Inaba‐Inoue, S., Yabuno, N., Sugiyama, A., Kumeta, H., & Ose, T. (2025) · Journal of Virology · doi:10.1128/jvi.00739-25

1H, 13C, and 15N resonance assignments and solution structure of the CID domain of SR-related- and CTD-associated factor 8 (SCAF8)

Dang, W., Muto, Y., He, F., Takahashi, M., Tsuda, K., Nagata, T., Tanaka, A., Kobayashi, N., Kigawa, T., Güntert, P., et al. (2025) · Biomolecular NMR Assignments · doi:10.1007/s12104-025-10252-3

Cyanobacterial Cyclic Peptides Containing cis ‐Pro Conformation

Haedar, J. R., Khan, A. H., Coxon, C. R., & Phan, C. (2026) · Chemistry - A European Journal · doi:10.1002/chem.202502932

A suite of macrocyclic peptide inhibitors and substrate probes for arginine methyltransferases

Yoshisada, R., Zhang, Y., Janssen, E., Bouchard, C., Poole, D. A., Wan, T., Soares, L., Houtkamp, I., Abeln, S., Mouhib, H., et al. (2026) · Chemical Science · doi:10.1039/d5sc09232a

Identification et caractérisation des modifications post-traductionnelles de la protéine TAU : implication dans le processus d'agrégation

Kamah, A. (2015) · theses.fr (ABES) · doi:10.70675/04392110zb087z42eez9ca0z62ea59984e5b

Etude des relations structurales et fonctionnelles entre le domaine 2 de la protéine NS5A du virus de l’hépatite C et la Cyclophiline A humaine

Dujardin, M. (2015) · theses.fr (ABES) · doi:10.70675/c69e4bebz6eb7z4a22zb1d5z6a6359ad722b

Protein Dynamics by Solid-State NMR with Ultra-Fast Magic-Angle Spinning : from Microcrystals to Amyloid Fibrils and Membrane Proteins

Marchand, T. L. (2018) · doi:10.70675/c0e7c0bdzceaez4e80z93b3z5a407f5e8d70

Synthèse de peptides bioactifs inspirés des venins

Giribaldi, J. (2019) · theses.fr (ABES) · doi:10.70675/4396528bz40f7z47abz935az5799907cf557

Interaction d’Engrailed avec des partenaires biologiques : FoxA2 et membranes lipidiques

Samson, D. (2018) · theses.fr (ABES) · doi:10.70675/ad7e294czeec6z4c4ez9ac4z46adf8859416

Structural Landscape of Syanodin I Lasso Peptide

Santos-Fernandez, M., Fouque, K. J. D., Karki, U., Blond, A., Idir, R., Asgharihosseinpour, N., Zirah, S., Chapagain, P. P., Mebel, A. M., Hegemann, J. D., et al. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00020

Conformational Analysis and Structural Characterization of Furin Inhibitors and Their Enzyme Complexes: Structural Insights into the Role of Cis/Trans Isomerization of the P2′–P3′ Peptide Bond

Dębowski, D., Helbik-Maciejewska, A., Gitlin‐Domagalska, A., Ptaszyńska, N., Łęgowska, A., Maszota‐Zieleniak, M., Samsonov, S. A., Zhukov, I., & Rolka, K. (2026) · Journal of Molecular Biology · doi:10.1016/j.jmb.2026.169848

Solution NMR study of the titin I-band IgI domain I82 shows unusual conformational dynamics

Kelly, C. M., Abukar, S., Gage, M. J., & Pfuhl, M. A. (2026) · Journal of Biomolecular NMR · doi:10.1007/s10858-026-00493-2

NMR study of human macroPARPs domains: 1H, 13C and 15N backbone and side-chain chemical shift assignments of hPARP9 macro domain 1 (MD1) in the apo and in the ADPr bound states

Moschidi, D., Fourkiotis, N. K., Tsatsouli, S.-A., Tsika, A. C., & Spyroulias, G. A. (2026) · Biomolecular NMR Assignments · doi:10.1007/s12104-026-10270-9

Backbone N ‐Methylation Improves PPCA‐Binding of a Stylissatin A Analogue via Conformational Modulation

Luthfiana, D., Dakiiwa, A., Shibata, T., & Kita, M. (2026) · Chemistry - An Asian Journal · doi:10.1002/asia.70906

Comprehensive solution NMR characterization of bivalirudin, a direct thrombin inhibitor peptide, and its process impurities by heteronuclear spectral fingerprinting at natural isotopic abundance

Mishra, S. H., Kaur, A., Vu, D., & Bhavaraju, S. (2026) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2026.117684

Insights into the molecular recognition of the second PDZ domain of ZO1 by coronavirus Envelope‐derived peptides

Toto, A., Pennacchietti, V., Isernia, C., Caldarelli, L., Malgieri, G., Gianni, S., Russo, L., Fattorusso, R., & Diana, D. (2026) · FEBS Journal · doi:10.1111/febs.70699

1H, 13C, and 15N backbone and side-chain resonance assignments of the Nostoc sp. H-NOX C139A variant in complex with the soluble Guanylyl Cyclase inhibitor Zinc Protoporphyrin IX

Γράβαλος, Σ., Andreadis, E. N., Cantini, F., Banci, L., & Spyroulias, G. A. (2026) · Biomolecular NMR Assignments · doi:10.1007/s12104-026-10274-5

Backbone and side chain 1H, 13C and 15N chemical shift assignment of the cargo-recognition domain MOTH of human TANGO1

Auch, J., Peddinghaus, A. C., & Stoll, R. (2026) · Biomolecular NMR Assignments · doi:10.1007/s12104-026-10278-1

1H, 13C, and 15N backbone resonance assignment of the N-terminal 280 amino acids of human NHERF1 proteinPreprint

Hornero-Romera, A., Treviño, M. Á., Pantoja‐Uceda, D., Millán, J., & Jiménez, M. Á. (2026) · Research Square · doi:10.21203/rs.3.rs-10664753/v1

NMR Structure and Dynamics of the Starfish Three-Finger Protein Lystar5

Paramonov, A. S., Shulepko, M. A., Chernikov, A. M., Kirpichnikov, M. P., Lyukmanova, E. N., & Shenkarev, Z. O. (2026) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162025605002

1H, 13C, and 15N resonance assignments and solution structure of the first double-stranded RNA-binding domain of DExH-Box Helicase 30 (DHX30)

Abe, C., Muto, Y., He, F., Takahashi, M., Tsuda, K., Nagata, T., Tanaka, A., Kobayashi, N., Kigawa, T., Güntert, P., et al. (2026) · Biomolecular NMR Assignments · doi:10.1007/s12104-026-10279-0

A Fluorogenic Cysteine‐Tetrapeptide Tagging Strategy for Nonperturbative Protein Labeling and Protein–Ligand Interaction Tracking

Wang, X., 潘星灿, Ying, Y., Bai, Z., Zhang, J., Shao, Z., Qian, J., Li, H., Zhang, N., Yang, F., et al. (2026) · Advanced Science · doi:10.1002/advs.78324

BindingDB Entry 50034054: Oligopeptide cyclophilin inhibitors: a reassessment.

BindingDB (2012) · UC San Diego · doi:10.7270/q2n87b59

BindingDB Entry 50045195: A potent HDAC inhibitor, 1-alaninechlamydocin, from a Tolypocladium sp. induces G2/M cell cycle arrest and apoptosis in MIA PaCa-2 cells.

BindingDB (2016) · UC San Diego · doi:10.7270/q29z96j4

BindingDB Entry 50034265: Disulfide and amide-bridged cyclic peptide analogues of the VEGF8¿?¿9¿? fragment: synthesis, conformational analysis and biological evaluation.

BindingDB (2012) · UC San Diego · doi:10.7270/q2hh6khg

1H, 13C, and 15N backbone resonance assignment of the N-terminal 280 amino acids of human NHERF1 protein

Hornero-Romera, A., Treviño, M. Á., Pantoja‐Uceda, D., Millán, J., & Jiménez, M. A. (2026) · Biomolecular NMR Assignments · doi:10.1007/s12104-026-10281-6

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Shen, Y., & Bax, A. (2009) · Journal of Biomolecular NMR · doi:10.1007/s10858-009-9395-y · Cited by 147

COMMUNICATION Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Shen, Y., & Bax, A. (2009)

Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Pahlke, D., Freund, C., Leitner, D., & Labudde, D. (2005) · BMC Structural Biology · doi:10.1186/1472-6807-5-8 · Cited by 39

NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: Mutants of staphylococcal nuclease with altered configuration at proline-117

Hinck, A. P., Eberhardt, E. S., & Markley, J. L. (1993) · Biochemistry · doi:10.1021/bi00095a009 · Cited by 30

The X‐Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides

Grathwohl, C., & Wüthrich, K. (1976) · Biopolymers · doi:10.1002/bip.1976.360151012 · Cited by 272