. Orcid, orcid Kátia

M. F. Lensink,

A. G. Raphaël and . Chaleil,

P. A. Bates,

A. Carbone,

S. Chang,

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

J. Fernandez-recio,

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

I. H. Moal,

. Maria-elisa-ruiz-echartea, . David-w.-ritchie, and . Isaure-chauvot-de-beauchêne, Author response for "Using Restraints in <scp>EROS?Dock</scp> Improves Model Quality in Pairwise and Multicomponent Protein Docking", Isaure Chauvot de Beauchêne, 2020.

Y. Shen,

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

A. Dasibekov, A. A. Yunusov, A. A. Yunusova, B. N. Korganbayev, N. A. Kuatbekov et al., SEALING OF A LAYER OF A SOUND WITH EFFECT OF ELASTIC PROPERTIES AND INHOMOGENEOUS BORDER CONDITIONS, PHYSICO-MATHEMATICAL SERIES, vol.4, issue.326, pp.42-49, 2019.

A. Ilya and . Vakser,

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

A. D. Duisenbay, N. Z. Takibayev, V. S. Vasilevsky, V. O. Kurmangaliyeva, and E. M. Akzhigitova, FORM FACTORS AND DENSITY DISTRIBUTIONS OF PROTONS AND NEUTRONS IN 7 Li AND 7 Be, PHYSICO-MATHEMATICAL SERIES, vol.3, issue.325, pp.71-76, 2019.

M. J. Alexandre and . Bonvin,

S. J. Wodak,

T. Ideker and R. Sharan, Protein networks in disease, Genome Research, vol.18, issue.4, pp.644-652, 2008.

A. Barabási, N. Gulbahce, and J. Loscalzo, Network medicine: a network-based approach to human disease, Nature Reviews Genetics, vol.12, issue.1, pp.56-68, 2010.

H. M. Berman, T. Battistuz, T. N. Bhat, W. F. Bluhm, P. E. Bourne et al., The Protein Data Bank, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.6, pp.899-907, 2002.

L. Lo-conte, C. Chothia, and J. Janin, The atomic structure of proteinprotein recognition sites, J Mol Biol, vol.285, issue.5, pp.2177-2198, 1999.

S. Dey, A. Pal, P. Chakrabarti, and J. Janin, The Subunit Interfaces of Weakly Associated Homodimeric Proteins, Journal of Molecular Biology, vol.398, issue.1, pp.146-160, 2010.

H. Ponstingl, . Thomas-kabir, D. Gorse, and J. M. Thornton, Morphological aspects of oligomeric protein structures, Progress in Biophysics and Molecular Biology, vol.89, issue.1, pp.9-35, 2005.

I. M. Nooren and J. M. Thornton, Structural Characterisation and Functional Significance of Transient Protein?Protein Interactions, Journal of Molecular Biology, vol.325, issue.5, pp.991-1018, 2003.

X. C. Bai, G. Mcmullan, and S. H. Scheres, How cryo-EM is revolutionizing structural biology, Trends in Biochemical Sciences, vol.40, issue.1, pp.49-57, 2015.

Y. Cheng, R. M. Glaeser, and E. Nogales, How Cryo-EM Became so Hot, Cell, vol.171, issue.6, pp.1229-1231, 2017.

P. J. Kundrotas, Z. Zhu, J. Janin, and I. A. Vakser, Templates are available to model nearly all complexes of structurally characterized proteins, Proceedings of the National Academy of Sciences, vol.109, issue.24, pp.9438-9441, 2012.

H. M. Berman, B. Coimbatore-narayanan, L. D. Costanzo, S. Dutta, S. Ghosh et al., Trendspotting in the Protein Data Bank, FEBS Letters, vol.587, issue.8, pp.1036-1045, 2013.

S. Ovchinnikov, H. Park, N. Varghese, P. Huang, G. A. Pavlopoulos et al., Protein structure determination using metagenome sequence data, Science, vol.355, issue.6322, pp.294-298, 2017.

D. S. Marks, T. A. Hopf, and C. Sander, Protein structure prediction from sequence variation, Nature Biotechnology, vol.30, issue.11, pp.1072-1080, 2012.

S. Ovchinnikov, D. E. Kim, R. Y. Wang, Y. Liu, F. Dimaio et al., Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta, Proteins: Structure, Function, and Bioinformatics, vol.84, issue.1, pp.67-75, 2016.

D. T. Jones, T. Singh, T. Kosciolek, and S. Tetchner, MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins, Bioinformatics, vol.31, issue.7, pp.999-1006, 2014.

J. P. Kocher, M. J. Rooman, and S. J. Wodak, Factors Influencing the Ability of Knowledge-based Potentials to Identify Native Sequence-Structure Matches, Journal of Molecular Biology, vol.235, issue.5, pp.1598-1613, 1994.

M. J. Rooman, J. P. Kocher, and S. J. Wodak, Prediction of protein backbone conformation based on seven structure assignments, Journal of Molecular Biology, vol.221, issue.3, pp.961-979, 1991.

M. J. Rooman, J. P. Kocher, and S. J. Wodak, Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions, Biochemistry, vol.31, issue.42, pp.10226-10238, 1992.

M. Rooman and S. J. Wodak, Generating and testing protein folds, Curr Opin Struct Biol, vol.3, issue.2, pp.247-259, 1993.

S. Min, B. Lee, and S. Yoon, Deep learning in bioinformatics, Briefings in Bioinformatics, vol.18, issue.5, p.bbw068, 2016.

S. Wang, S. Sun, Z. Li, R. Zhang, and J. Xu, Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model, PLOS Computational Biology, vol.13, issue.1, p.e1005324, 2017.

D. Guzenko, A. Lafita, B. Monastyrskyy, A. Kryshtafovych, and J. M. Duarte, Assessment of protein assembly prediction in CASP13, Proteins: Structure, Function, and Bioinformatics, vol.87, issue.12, pp.1190-1199, 2019.

T. A. Whitehead, D. Baker, and S. J. Fleishman, Computational Design of Novel Protein Binders and Experimental Affinity Maturation, Methods in Enzymology, vol.523, pp.1-19, 2013.

T. A. Whitehead, A. Chevalier, Y. A. Song, C. Dreyfus, S. J. Fleishman et al., Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing, Nature Biotechnology, vol.30, issue.6, pp.543-548, 2012.

D. A. Silva, S. Yu, U. Y. Ulge, J. B. Spangler, K. M. Jude et al., De novo design of potent and selective mimics of IL-2 and IL-15, Nature, vol.565, issue.7738, pp.186-191, 2019.

T. O. Yeates, Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials, Annual Review of Biophysics, vol.46, issue.1, pp.23-42, 2017.

A. B. Ward, A. Sali, and I. A. Wilson, Biochemistry. Integrative structural biology. Science, vol.339, issue.6122, pp.913-915, 2013.

B. Webb, S. Viswanath, and M. Bonomi, Integrative structure modeling with the integrative modeling platform, Protein Sci, vol.27, issue.1, pp.245-258, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-02406448

S. J. Wodak and J. Janin, Structural basis of macromolecular recognition, Advances in Protein Chemistry, vol.61, pp.9-73, 2002.

D. W. Ritchie, Recent progress and future directions in protein-protein docking, Curr Protein Pept Sci, vol.9, issue.1, pp.1-15, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00434268

S. Vajda and D. Kozakov, Convergence and combination of methods in protein?protein docking, Current Opinion in Structural Biology, vol.19, issue.2, pp.164-170, 2009.

S. J. Fleishman, T. A. Whitehead, and E. M. Strauch, Community-wide assessment of protein-interface modeling suggests improvements to design methodology, J Mol Biol, vol.414, issue.2, pp.289-302, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00637848

R. Moretti, S. J. Fleishman, and R. Agius, Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Proteins, vol.81, issue.11, pp.1980-1987, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00905794

M. F. Lensink and S. J. Wodak, Docking, scoring, and affinity prediction in CAPRI, Proteins, vol.81, issue.12, pp.2082-2095, 2013.

M. F. Lensink, I. H. Moal, and P. A. Bates, Blind prediction of interfacial water positions in CAPRI, Proteins, vol.82, issue.4, pp.620-632, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00880345

Q. Xu, A. A. Canutescu, G. Wang, M. Shapovalov, Z. Obradovic et al., Statistical analysis of interface similarity in crystals of homologous proteins, J Mol Biol, vol.381, issue.2, pp.487-507, 2008.

E. D. Levy and S. A. Teichmann, Structural, Evolutionary, and Assembly Principles of Protein Oligomerization, Progress in Molecular Biology and Translational Science, vol.117, pp.25-51, 2013.

J. Negroni, R. Mosca, and P. Aloy, Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone, Structure, vol.22, issue.9, pp.1356-1362, 2014.

A. Szilagyi and Y. Zhang, Template-based structure modeling of protein?protein interactions, Current Opinion in Structural Biology, vol.24, pp.10-23, 2014.

M. F. Lensink, S. Velankar, and A. Kryshtafovych, Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Proteins, vol.84, issue.1, pp.323-348, 2016.

M. F. Lensink, S. Velankar, M. Baek, L. Heo, C. Seok et al., The challenge of modeling protein assemblies: the CASP12-CAPRI experiment, Proteins, vol.86, issue.1, pp.257-273, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02389365

A. Lafita, S. Bliven, and A. Kryshtafovych, Assessment of protein assembly prediction in CASP12, Proteins, vol.86, issue.1, pp.247-256, 2018.

M. F. Lensink, R. Mendez, and S. J. Wodak, Docking and scoring protein complexes: CAPRI, Proteins, vol.69, issue.4, pp.704-718, 2007.

M. F. Lensink and S. J. Wodak, Docking and scoring protein interactions: CAPRI 2009, Proteins: Structure, Function, and Bioinformatics, vol.78, issue.15, pp.3073-3084, 2010.

M. Remmert, A. Biegert, A. Hauser, and J. Soding, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat Methods, vol.9, issue.2, pp.173-175, 2012.

L. Zimmermann, A. Stephens, and S. Z. Nam, A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core, J Mol Biol, vol.430, issue.15, pp.2237-2243, 2018.

M. F. Lensink and S. J. Wodak, Blind predictions of protein interfaces by docking calculations in CAPRI, Proteins, vol.78, issue.15, pp.3085-3095, 2010.

E. Krissinel and K. Henrick, Inference of macromolecular assemblies from crystalline state, J Mol Biol, vol.372, issue.3, pp.774-797, 2007.

S. Bliven, A. Lafita, A. Parker, G. Capitani, and J. M. Duarte, Automated evaluation of quaternary structures from protein crystals, PLoS Comput Biol, vol.14, issue.4, p.1006104, 2018.

J. Soding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-960, 2005.

A. Hildebrand, M. Remmert, A. Biegert, and J. Soding, Fast and accurate automatic structure prediction with HHpred, Proteins, vol.77, issue.9, pp.128-132, 2009.

M. F. Lensink, S. Velankar, and S. J. Wodak, Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition, Proteins: Structure, Function, and Bioinformatics, vol.85, issue.3, pp.359-377, 2016.

A. Berchanski and M. Eisenstein, Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry, Proteins, vol.53, issue.4, pp.817-829, 2003.

B. Pierce, W. Tong, and Z. Weng, M-ZDOCK: a grid-based approach for Cn symmetric multimer docking, Bioinformatics, vol.21, issue.8, pp.1472-1478, 2005.

D. W. Ritchie and S. Grudinin, Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry, Journal of Applied Crystallography, vol.49, issue.1, pp.158-167, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01261402

E. Mashiach, D. Schneidman-duhovny, A. Peri, Y. A. Shavit, R. Nussinov et al., An integrated suite of fast docking algorithms, Proteins: Structure, Function, and Bioinformatics, vol.78, issue.15, pp.3197-3204, 2010.

D. Kozakov, D. R. Hall, B. Xia, K. A. Porter, D. Padhorny et al., The ClusPro web server for protein?protein docking, Nature Protocols, vol.12, issue.2, pp.255-278, 2017.

S. R. Comeau and C. J. Camacho, Predicting oligomeric assemblies: N-mers a primer, Journal of Structural Biology, vol.150, issue.3, pp.233-244, 2005.

S. Basu and B. Wallner, DockQ: A Quality Measure for Protein-Protein Docking Models, PLOS ONE, vol.11, issue.8, p.e0161879, 2016.

L. X. Peterson, A. Roy, C. Christoffer, G. Terashi, and D. Kihara, Modeling disordered protein interactions from biophysical principles, PLOS Computational Biology, vol.13, issue.4, p.e1005485, 2017.

S. J. De-vries and A. M. Bonvin, How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes, Current Protein & Peptide Science, vol.9, issue.4, pp.394-406, 2008.

B. Webb and A. Sali, Protein Structure Modeling with MODELLER, Methods in Molecular Biology, vol.1654, pp.39-54, 2017.

J. Dapk?nas, A. Timinskas, K. Olechnovi?, M. Margelevi?ius, R. Di?i?nas et al., The PPI3D web server for searching, analyzing and modeling protein?protein interactions in the context of 3D structures, Bioinformatics, vol.33, issue.6, p.btw756, 2016.

K. Olechnovi? and ?. Venclovas, VoroMQA: Assessment of protein structure quality using interatomic contact areas, Proteins: Structure, Function, and Bioinformatics, vol.85, issue.6, pp.1131-1145, 2017.

H. Zhou and J. Skolnick, GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction, Biophysical Journal, vol.101, issue.8, pp.2043-2052, 2011.

H. Zhou and Y. Zhou, Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction, Protein Science, vol.11, issue.11, pp.2714-2726, 2009.

S. Y. Huang and X. Zou, Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures, Proteins: Structure, Function, and Bioinformatics, vol.79, issue.9, pp.2648-2661, 2011.

P. J. Kundrotas, I. Anishchenko, V. D. Badal, M. Das, T. Dauzhenka et al., Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function, Proteins: Structure, Function, and Bioinformatics, vol.86, issue.1, pp.302-310, 2017.

E. Chermak, A. Petta, L. Serra, A. Vangone, V. Scarano et al., CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts, Bioinformatics, vol.31, issue.9, pp.1481-1483, 2014.

D. W. Ritchie and G. J. Kemp, Protein docking using spherical polar Fourier correlations, Proteins: Structure, Function, and Genetics, vol.39, issue.2, pp.178-194, 2000.
URL : https://hal.archives-ouvertes.fr/inria-00434273

M. El-houasli, B. Maigret, M. D. Devignes, A. W. Ghoorah, S. Grudinin et al., Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models, Proteins: Structure, Function, and Bioinformatics, vol.85, issue.3, pp.463-469, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01388654

Y. Yan, H. Tao, and S. Y. Huang, HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry, Nucleic Acids Research, vol.46, issue.W1, pp.W423-W431, 2018.

J. Esquivel-rodríguez, Y. D. Yang, and D. Kihara, Multi-LZerD: Multiple protein docking for asymmetric complexes, Proteins: Structure, Function, and Bioinformatics, vol.80, issue.7, pp.1818-1833, 2012.

M. F. Lensink, G. Brysbaert, N. Nadzirin, S. Velankar, R. A. Chaleil et al., Blind prediction of homo? and hetero?protein complexes: The CASP13?CAPRI experiment, Proteins: Structure, Function, and Bioinformatics, vol.87, issue.12, pp.1200-1221, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02320974