REFERENCES
1. Moult J, Pedersen JT, Judson R,
Fidelis K. A large-scale experiment to assess protein structure
prediction methods. Proteins 1995;23(3):ii-v.
2. Moult J, Fidelis K, Kryshtafovych
A, Schwede T, Tramontano A. Critical assessment of methods of protein
structure prediction (CASP)-Round XII. Proteins 2018;86 Suppl 1:7-15.
3. Kryshtafovych A, Schwede T, Topf M,
Fidelis K, Moult J. Critical assessment of methods of protein structure
prediction (CASP)-Round XIII. Proteins 2019;87(12):1011-1020.
4. Kryshtafovych A, Schwede T, Topf M,
Fidelis K, Moult J. Critical assessment of methods of protein structure
prediction (CASP)-Round XIV. Proteins-Structure Function and
Bioinformatics 2021;89(12):1607-1617.
5. Cheng H, Schaeffer RD, Liao Y,
Kinch LN, Pei J, Shi S, Kim BH, Grishin NV. ECOD: an evolutionary
classification of protein domains. PLoS Comput Biol
2014;10(12):e1003926.
6. Kinch LN, Shi S, Cheng H, Cong Q,
Pei J, Mariani V, Schwede T, Grishin NV. CASP9 target classification.
Proteins 2011;79 Suppl 10:21-36.
7. Kinch LN, Li W, Schaeffer RD,
Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV. CASP 11 target
classification. Proteins 2016;84 Suppl 1:20-33.
8. Abriata LA, Kinch LN, Tamo GE,
Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Definition and
classification of evaluation units for tertiary structure prediction in
CASP12 facilitated through semi-automated metrics. Proteins 2018;86
Suppl 1:16-26.
9. Kinch LN, Kryshtafovych A,
Monastyrskyy B, Grishin NV. CASP13 target classification into tertiary
structure prediction categories. Proteins 2019;87(12):1021-1036.
10. Kinch LN, Schaeffer RD,
Kryshtafovych A, Grishin NV. Target classification in the 14th round of
the critical assessment of protein structure prediction (CASP14).
Proteins-Structure Function and Bioinformatics 2021;89(12):1618-1632.
11. Zemla A. LGA: A method for
finding 3D similarities in protein structures. Nucleic Acids Res
2003;31(13):3370-3374.
12. Xu Y, Xu D, Gambow HN. Protein
domain decomposition using a graph-theoretic approach. Bioinformatics
2000;16(12):1091-1104.
13. Zhou HY, Xue B, Zhou YQ. DDOMAIN:
Dividing structures into domains using a normalized domain-domain
interaction profile. Protein Science 2007;16(5):947-955.
14. Postic G, Ghouzam Y, Chebrek R,
Gelly JC. An ambiguity principle for assigning protein structural
domains. Sci Adv 2017;3(1).
15. Cretin G, Galochkina T, Vander
Meersche Y, de Brevern AG, Postic G, Gelly JC. SWORD2: hierarchical
analysis of protein 3D structures. Nucleic Acids Research
2022;50(W1):W732-W738.
16. Altschul SF, Madden TL, Schaffer
AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a
new generation of protein database search programs. Nucleic Acids Res
1997;25(17):3389-3402.
17. Remmert M, Biegert A, Hauser A,
Soding J. HHblits: lightning-fast iterative protein sequence searching
by HMM-HMM alignment. Nat Methods 2012;9(2):173-175.
18. Steinegger M, Meier M, Mirdita M,
Vohringer H, Haunsberger SJ, Soding J. HH-suite3 for fast remote
homology detection and deep protein annotation. BMC Bioinformatics
2019;20(1):473.
19. van Kempen M, Kim SH, Tumescheit
C, Mirdita M, Gilchrist C, Söding J, Steinegger M. Foldseek: fast and
accurate protein structure search. bioRxiv 2022.
20. Taylor TJ, Tai CH, Huang YJ,
Block J, Bai H, Kryshtafovych A, Montelione GT, Lee B. Definition and
classification of evaluation units for CASP10. Proteins 2014;82 Suppl
2:14-25.
21. Rigden DJ, al e. Tertiary
structure assessment in CASP15. Proteins 2023(This issue).
22. Schrodinger L, DeLano WL. PyMOL.
Available at: wwwpymolorg 2020.
23. Banneville AS, de la Tour CB, De
Bonis S, Hognon C, Colletier JP, Teulon JM, Le Roy A, Pellequer JL,
Monari A, Dehez F, Confalonieri F, Servant P, Timmins J. Structural and
functional characterization of DdrC, a novel DNA damage-induced nucleoid
associated protein involved in DNA compaction. Nucleic Acids Research
2022;50(13):7680-7696.
24. Deep A, Gu YJ, Gao YQ, Ego KM,
Herzik MA, Zhou HL, Corbett KD. The SMC-family Wadjet complex protects
bacteria from plasmid transformation by recognition and cleavage of
closed-circular DNA. Molecular Cell 2022;82(21):4145-+.
25. Wald J, Fahrenkamp D,
Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC.
Mechanism of AAA plus ATPase-mediated RuvAB-Holliday junction branch
migration. Nature 2022;609(7927):630-+.
26. Ford RC, Beis K. Learning the
ABCs one at a time: structure and mechanism of ABC transporters. Biochem
Soc T 2019;47:23-36.
27. Photenhauer A, Cerqueira F,
Villafuerte-Vega R, Armbruster K, Mareček F, Chen T, Wawrzak Z, Hopkins
J, Vander Kooi C, Janeček Š, Ruotolo B, Koropatkin N. The Ruminococcus
bromii amylosome protein Sas6 binds single and double helical α-glucan
structures in starch. bioRxiv 2022.
28. Liu S, Xia X, Calvo E, Zhou Z.
Native structure of mosquito salivary protein uncovers domains relevant
to pathogen transmission. Nature Communications 2023;14(899).
29. Kryshtafovych A, Schwede T, Topf
M, Fidelis K, Moult J. Critical assessment of methods of protein
structure prediction (CASP)-Round XV. Proteins 2023(This issue).
30. Jumper J, Evans R, Pritzel A,
Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Zidek A,
Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A,
Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman
D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T,
Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D.
Applying and improving AlphaFold at CASP14. Proteins-Structure Function
and Bioinformatics 2021;89(12):1711-1721.
31. Jumper J, Evans R, Pritzel A,
Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Zidek A,
Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A,
Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman
D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T,
Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P,
Hassabis D. Highly accurate protein structure prediction with AlphaFold.
Nature 2021;596(7873):583.