References
1. 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.
2. Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C,
Žídek A, Nelson AWR, Bridgland A, Penedones H, Petersen S, Simonyan K,
Crossan S, Kohli P, Jones DT, Silver D, Kavukcuoglu K, Hassabis D.
Protein structure prediction using multiple deep neural networks in the
13th Critical Assessment of Protein Structure Prediction (CASP13).
Proteins 2019;87(12):1141–1148.
3. Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C,
Žídek A, Nelson AWR, Bridgland A, Penedones H, Petersen S, Simonyan K,
Crossan S, Kohli P, Jones DT, Silver D, Kavukcuoglu K, Hassabis D.
Improved protein structure prediction using potentials from deep
learning. Nature 2020;577(7792):706–710.
4. Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D.
Improved protein structure prediction using predicted interresidue
orientations. Proc Natl Acad Sci U S A 2020;117(3):1496–1503.
5. Keskin O, Tuncbag N, Gursoy A. Predicting Protein-Protein
Interactions from the Molecular to the Proteome Level. Chem Rev
2016;116(8):4884–4909.
6. Luck K, Kim D-K, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R,
Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M,
Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp
JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C,
Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha
O, Bowman-Colin C, Chin S-F, Choi SG, Colabella C, Coppin G, D’Amata C,
De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F,
Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y,
Landini S, Li R, Lieshout N van, MacWilliams A, Markey D, Paulson JN,
Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y,
Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe
V, Twizere J-C, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X,
Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao
T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. A
reference map of the human binary protein interactome. Nature
2020;580(7803):402–408.
7. Aloy P, Russell RB. Ten thousand interactions for the molecular
biologist. Nat Biotechnol 2004;22(10):1317–1321.
8. Garma L, Mukherjee S, Mitra P, Zhang Y. How many protein-protein
interactions types exist in nature? PLoS One 2012;7(6):e38913.
9. Aloy P, Ceulemans H, Stark A, Russell RB. The relationship between
sequence and interaction divergence in proteins. J Mol Biol
2003;332(5):989–998.
10. Lensink MF, Nadzirin N, Velankar S, Wodak SJ. Modeling
protein-protein, protein-peptide, and protein-oligosaccharide complexes:
CAPRI 7th edition. Proteins 2020;88(8):916–938.
11. Lensink MF, Velankar S, Kryshtafovych A, Huang S-Y,
Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath
S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L,
Rie Lee G, Seok C, Qin S, Zhou H-X, Ritchie DW, Maigret B, Devignes M-D,
Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M,
Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F,
Guerois R, Vangone A, Rodrigues JPGLM, Zundert G van, Nellen M, Xue L,
Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X,
Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim H-R,
Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC,
Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda
T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B,
Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D,
Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T,
Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ,
Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of
homoprotein and heteroprotein complexes by protein docking and
template-based modeling: A CASP-CAPRI experiment. Proteins 2016;84 Suppl
1:323–348.
12. Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG,
Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu R-R, Xu
X-M, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka
E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A,
Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang S-Y, Rosell
M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L,
Fernandez-Recio J, Christoffer C, Terashi G, Shin W-H, Aderinwale T,
Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K,
Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie
DW, Chauvot de Beauchêne I, Maigret B, Devignes M-D, Ruiz Echartea ME,
Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M,
Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D,
Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S,
Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T,
Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J,
Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J,
Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L,
Jiménez-García B, Noort CW van, Honorato RV, Bonvin AMJJ, Wodak SJ.
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI
experiment. Proteins 2019;87(12):1200–1221.
13. Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B,
Duarte JM, Schwede T, Capitani G. Assessment of protein assembly
prediction in CASP12. Proteins 2018;86 Suppl 1:247–256.
14. Guzenko D, Lafita A, Monastyrskyy B, Kryshtafovych A, Duarte JM.
Assessment of protein assembly prediction in CASP13. Proteins
2019;87(12):1190–1199.
15. Dapkūnas J, Olechnovič K, Venclovas Č. Modeling of protein complexes
in CAPRI Round 37 using template-based approach combined with model
selection. Proteins 2018;86 Suppl 1:292–301.
16. Dapkūnas J, Kairys V, Olechnovič K, Venclovas Č. Template-based
modeling of diverse protein interactions in CAPRI rounds 38-45. Proteins
2020;88(8):939–947.
17. Dapkūnas J, Olechnovič K, Venclovas Č. Structural modeling of
protein complexes: Current capabilities and challenges. Proteins
2019;87(12):1222–1232.
18. Dapkūnas J, Timinskas A, Olechnovič K, Margelevičius M, Dičiūnas R,
Venclovas Č. The PPI3D web server for searching, analyzing and modeling
protein-protein interactions in the context of 3D structures.
Bioinformatics 2017;33(6):935–937.
19. Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M,
Gabler F, Söding J, Lupas AN, Alva V. A Completely Reimplemented MPI
Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol
2018;430(15):2237–2243.
20. Söding J. Protein homology detection by HMM-HMM comparison.
Bioinformatics 2005;21(7):951–960.
21. Holm L. DALI and the persistence of protein shape. Protein Sci
2020;29(1):128–140.
22. Šali A, Blundell TL. Comparative Protein Modelling by Satisfaction
of Spatial Restraints. J Mol Biol 1993;234(3):779–815.
23. Janson G, Grottesi A, Pietrosanto M, Ausiello G, Guarguaglini G,
Paiardini A. Revisiting the “satisfaction of spatial restraints”
approach of MODELLER for protein homology modeling. PLoS Comput Biol
2019;15(12):e1007219.
24. Zhang Y, Skolnick J. TM-align: a protein structure alignment
algorithm based on the TM-score. Nucleic Acids Res
2005;33(7):2302–2309.
25. Trigg J, Gutwin K, Keating AE, Berger B. Multicoil2: predicting
coiled coils and their oligomerization states from sequence in the
twilight zone. PLoS One 2011;6(8):e23519.
26. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier
correlations. Proteins 2000;39(2):178–194.
27. Ritchie DW, Grudinin S. Spherical polar Fourier assembly of protein
complexes with arbitrary point group symmetry. J Appl Cryst
2016;49(1):158–167.
28. Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA,
Wang L-P, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR,
Pande VS. OpenMM 7: Rapid development of high performance algorithms for
molecular dynamics. PLoS Comput Biol 2017;13(7):e1005659.
29. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C.
Comparison of multiple Amber force fields and development of improved
protein backbone parameters. Proteins 2006;65(3):712–725.
30. Onufriev A, Bashford D, Case DA. Exploring protein native states and
large-scale conformational changes with a modified generalized born
model. Proteins 2004;55(2):383–394.
31. Olechnovič K, Kulberkytė E, Venclovas Č. CAD-score: a new contact
area difference-based function for evaluation of protein structural
models. Proteins 2013;81(1):149–162.
32. Olechnovič K, Venclovas Č. Contact Area-Based Structural Analysis of
Proteins and Their Complexes Using CAD-Score. Methods Mol Biol
2020;2112:75–90.
33. Olechnovič K, Venclovas Č. VoroMQA web server for assessing
three-dimensional structures of proteins and protein complexes. Nucleic
Acids Res 2019;47(W1):W437–W442.
34. Olechnovič K, Venclovas Č. VoroMQA: Assessment of protein structure
quality using interatomic contact areas. Proteins 2017;85(6):1131–1145.
35. Olechnovič K, Venclovas Č. Voronota: A fast and reliable tool for
computing the vertices of the Voronoi diagram of atomic balls. J Comput
Chem 2014;35(8):672–681.
36. Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T. Modeling
protein quaternary structure of homo- and hetero-oligomers beyond binary
interactions by homology. Sci Rep 2017;7(1):10480.
37. Méndez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind
predictions of protein-protein interactions: current status of docking
methods. Proteins 2003;52(1):51–67.
38. Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local
superposition-free score for comparing protein structures and models
using distance difference tests. Bioinformatics 2013;29(21):2722–2728.
39. Zhang Y, Skolnick J. Scoring function for automated assessment of
protein structure template quality. Proteins 2004;57(4):702–710.
40. Mukherjee S, Zhang Y. MM-align: a quick algorithm for aligning
multiple-chain protein complex structures using iterative dynamic
programming. Nucleic Acids Res 2009;37(11):e83.
41. Sela-Culang I, Kunik V, Ofran Y. The structural basis of
antibody-antigen recognition. Front Immunol 2013;4:302.
42. Grinter R, Morris FC, Dunstan RA, Leung PM, Belousoff M, Gunasinghe
SD, Beckham S, Peleg AY, Greening C, Li J, Heinz E, Lithgow T. BonA from
Acinetobacter baumannii forms a divisome-localized decamer that supports
outer envelope function. bioRxiv 2020:2020.09.01.278697.
43. Song Y, DiMaio F, Wang RY-R, Kim D, Miles C, Brunette T, Thompson J,
Baker D. High-resolution comparative modeling with RosettaCM. Structure
2013;21(10):1735–1742.
44. Altschul SF, Madden TL, Schäffer 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.
45. Fernández-Recio J, Totrov M, Abagyan R. Identification of
protein-protein interaction sites from docking energy landscapes. J Mol
Biol 2004;335(3):843–865.
46. Viswanathan R, Fajardo E, Steinberg G, Haller M, Fiser A.
Protein-protein binding supersites. PLoS Comput Biol
2019;15(1):e1006704.
47. Kurkcuoglu Z, Bonvin AMJJ. Pre- and post-docking sampling of
conformational changes using ClustENM and HADDOCK for protein-protein
and protein-DNA systems. Proteins 2020;88(2):292–306.
48. Zeng H, Wang S, Zhou T, Zhao F, Li X, Wu Q, Xu J. ComplexContact: a
web server for inter-protein contact prediction using deep learning.
Nucleic Acids Res 2018;46(W1):W432–W437.
49. Szurmant H, Weigt M. Inter-residue, inter-protein and inter-family
coevolution: bridging the scales. Curr Opin Struct Biol 2018;50:26–32.
50. Faure G, Andreani J, Guerois R. InterEvol database: exploring the
structure and evolution of protein complex interfaces. Nucleic Acids Res
2012;40(Database issue):D847-856.
51. Uguzzoni G, John Lovis S, Oteri F, Schug A, Szurmant H, Weigt M.
Large-scale identification of coevolution signals across homo-oligomeric
protein interfaces by direct coupling analysis. Proc Natl Acad Sci U S A
2017;114(13):E2662–E2671.
52. Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA.
Principles of assembly reveal a periodic table of protein complexes.
Science 2015;350(6266):aaa2245.