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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, 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 HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, 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 JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, 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.

Proteins. 2016 Apr 28. doi: 10.1002/prot.25007. [Epub ahead of print]


Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

Calvanese L, D'Auria G, Vangone A, Falcigno L, Oliva R.

J Struct Biol. 2016 Jun;194(3):317-24. doi: 10.1016/j.jsb.2016.03.008. Epub 2016 Mar 9.


Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet.

Chawla M, Credendino R, Chermak E, Oliva R, Cavallo L.

J Phys Chem B. 2016 Mar 10;120(9):2216-24. doi: 10.1021/acs.jpcb.6b00125. Epub 2016 Feb 25.


The "omics" of human male infertility: integrating big data in a systems biology approach.

Carrell DT, Aston KI, Oliva R, Emery BR, De Jonge CJ.

Cell Tissue Res. 2016 Jan;363(1):295-312. doi: 10.1007/s00441-015-2320-7. Epub 2015 Dec 10.


Allele mining and enhanced genetic recombination for rice breeding.

Leung H, Raghavan C, Zhou B, Oliva R, Choi IR, Lacorte V, Jubay ML, Cruz CV, Gregorio G, Singh RK, Ulat VJ, Borja FN, Mauleon R, Alexandrov NN, McNally KL, Sackville Hamilton R.

Rice (N Y). 2015 Dec;8(1):34. doi: 10.1186/s12284-015-0069-y. Epub 2015 Nov 25.


Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R.

PLoS One. 2015 Sep 30;10(9):e0139256. doi: 10.1371/journal.pone.0139256. eCollection 2015.


Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules.

Chawla M, Credendino R, Oliva R, Cavallo L.

J Phys Chem B. 2015 Oct 15;119(41):12982-9. doi: 10.1021/acs.jpcb.5b06861. Epub 2015 Oct 1.


An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Chawla M, Oliva R, Bujnicki JM, Cavallo L.

Nucleic Acids Res. 2015 Oct 30;43(19):9573. doi: 10.1093/nar/gkv925. Epub 2015 Sep 10. No abstract available.


The D173G mutation in ADAMTS-13 causes a severe form of congenital thrombotic thrombocytopenic purpura. A clinical, biochemical and in silico study.

Lancellotti S, Peyvandi F, Pagliari MT, Cairo A, Abdel-Azeim S, Chermak E, Lazzareschi I, Mastrangelo S, Cavallo L, Oliva R, De Cristofaro R.

Thromb Haemost. 2016 Jan;115(1):51-62. doi: 10.1160/TH15-02-0119. Epub 2015 Aug 13.


Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.

Oliva R, Chermak E, Cavallo L.

Molecules. 2015 Jul 1;20(7):12045-60. doi: 10.3390/molecules200712045. Review.


An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Chawla M, Oliva R, Bujnicki JM, Cavallo L.

Nucleic Acids Res. 2015 Aug 18;43(14):6714-29. doi: 10.1093/nar/gkv606. Epub 2015 Jun 27. Erratum in: Nucleic Acids Res. 2015 Oct 30;43(19):9573.


Update on Bacterial Blight of Rice: Fourth International Conference on Bacterial Blight.

Sundaram RM, Chatterjee S, Oliva R, Laha GS, Cruz CV, Leach JE, Sonti RV.

Rice (N Y). 2014 Dec;7(1):12. doi: 10.1186/s12284-014-0012-7. Epub 2014 Jul 26.


Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems.

Dossa GS, Sparks A, Cruz CV, Oliva R.

Front Plant Sci. 2015 May 5;6:305. doi: 10.3389/fpls.2015.00305. eCollection 2015.


Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility.

Castillo J, Estanyol JM, Ballescá JL, Oliva R.

Asian J Androl. 2015 Jul-Aug;17(4):601-9. doi: 10.4103/1008-682X.153302. Review.


Advances in sperm proteomics: best-practise methodology and clinical potential.

Codina M, Estanyol JM, Fidalgo MJ, Ballescà JL, Oliva R.

Expert Rev Proteomics. 2015 Jun;12(3):255-77. doi: 10.1586/14789450.2015.1040769. Epub 2015 Apr 28. Review.


The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.

Pantano L, Jodar M, Bak M, Ballescà JL, Tommerup N, Oliva R, Vavouri T.

RNA. 2015 Jun;21(6):1085-95. doi: 10.1261/rna.046482.114. Epub 2015 Apr 22.


A Recent Expansion of the RXLR Effector Gene Avrblb2 Is Maintained in Global Populations of Phytophthora infestans Indicating Different Contributions to Virulence.

Oliva RF, Cano LM, Raffaele S, Win J, Bozkurt TO, Belhaj K, Oh SK, Thines M, Kamoun S.

Mol Plant Microbe Interact. 2015 Aug;28(8):901-12. doi: 10.1094/MPMI-12-14-0393-R. Epub 2015 Jul 17.


Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS).

Paiva C, Amaral A, Rodriguez M, Canyellas N, Correig X, Ballescà JL, Ramalho-Santos J, Oliva R.

Andrology. 2015 May;3(3):496-505. doi: 10.1111/andr.12027. Epub 2015 Apr 8.


Comparative analysis of boar seminal plasma proteome from different freezability ejaculates and identification of Fibronectin 1 as sperm freezability marker.

Vilagran I, Yeste M, Sancho S, Castillo J, Oliva R, Bonet S.

Andrology. 2015 Mar;3(2):345-56. doi: 10.1111/andr.12009. Epub 2015 Feb 9.


CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts.

Chermak E, Petta A, Serra L, Vangone A, Scarano V, Cavallo L, Oliva R.

Bioinformatics. 2015 May 1;31(9):1481-3. doi: 10.1093/bioinformatics/btu837. Epub 2014 Dec 21.

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