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Accueil > Recherche > Equipes de recherche > Computational Molecular Systems Biology > Publications

Computational Molecular Systems Biology

2016

On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes.
Copie G, Cleri F, Blossey R, Lensink MF.
Sci Rep. 2016 Dec 1 ;6:38259. doi : 10.1038/srep38259.

Modeling protein-protein and protein-peptide complexes : CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ.
Proteins. 2016 Nov 16. doi : 10.1002/prot.25215.

Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models.
Chermak E, De Donato R, Lensink MF, Petta A, Serra L, Scarano V, Cavallo L,
Oliva R.
PLoS One. 2016 Nov 15 ;11(11):e0166460. doi:10.1371/journal.pone.0166460.

CLUB-MARTINI : Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.
Hou Q, Lensink MF, Heringa J, Feenstra KA.
PLoS One. 2016 May 11 ;11(5):e0155251. doi:10.1371/journal.pone.0155251.

Beyond Poisson-Boltzmann : fluctuations and fluid structure in a self-consistent theory
Sahin Buyukdagli, Ralf Blossey
Journal of Physics : Condensed Matter 28, 343001 (2016)

Core-oscillator model of Caulobacter crescentus
Yves Vandecan, Emanuele Biondi, Ralf Blossey
Physical Review E 93, 063413 (2016)

Correlation-induced DNA adsorption on like-charged membranes
Sahin Buyukdagli, Ralf Blossey
Physical Review E 94, 042502 (2016)

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.

Molecular docking as a popular tool in drug design, an in silico travel
de Ruyck J, Brysbaert G, Blossey R, Lensink MF. Adv Appl Bioinform Chem. 2016 Jun
28 ;9:1-11. doi : 10.2147/AABC.S105289. eCollection 2016. Review. PubMed PMID :
27390530

Affinity of Glycan-Modified Nanodiamonds towards Lectins and Uropathogenic Escherichia Coli Volodymyr Turcheniuk, Kostiantyn Turcheniuk, Julie Bouckaert, Alexandre Barras, Tetiana Dumych, Rostyslav Bilyy, Vladimir Zaitsev, Aloysius Siriwardena, Qi Wang, Rabah Boukherroub, and Sabine Szunerits. ChemNanoMat 2016, 2, 307–314. DOI:10.1002/cnma.201500229

Particle-based photodynamic therapy based on indocyanine green modified plasmonic nanostructures for inactivation of a Crohn’s disease-associated Escherichia coli strain
Roxana Jijie ab, Tetiana Dumych c, Li Chengnan a, Julie Bouckaert c, Kostiantyn Turcheniuk a, Charles-Henri Hage df, Laurent Heliot df, Benoit Cudennec e, Nicoleta Dumitrascu b, Rabah Boukherroub a and Sabine Szunerits. DOI : 10.1039/C5TB02697K (Paper) J. Mater. Chem. B, 2016, 4, 2598-2605

A library of heptyl mannose-functionalized copolymers with distinct compositions, microstructures and neighboring non-sugar motifs as potent antiadhesives of type 1 piliated E. coli.
Xibo Yan abc, Adeline Sivignon de, Nicolas Barnich de, Sébastien G. Gouin f, Julie Bouckaert g, Etienne Fleury abc and Julien Bernard. DOI : 10.1039/C6PY00118A (Paper) Polym. Chem., 2016, 7, 2674-2683

Plasmonic photothermal cancer therapy with gold nanorods/reduced graphene oxide core/shell nanocomposites
Kostiantyn Turcheniuka, Tetiana Dumychb, Rostyslav Bilyybc, Volodymyr Turcheniukad, Julie Bouckaertb, Volodymyr Vovkc, Valentyna Chopyakc, Vladimir Zaitsevde, Pascal Mariotf, Natasha Prevarskayaf, Rabah Boukherrouba and Sabine Szunerits. DOI : 10.1039/C5RA24662H (Paper) RSC Adv., 2016, 6, 1600-1610

Differentiation of Crohn’s Disease-Associated Isolates from Other Pathogenic
Escherichia coli by Fimbrial Adhesion under Shear Force. Biology (Basel).
Szunerits S, Zagorodko O, Cogez V, Dumych T, Chalopin T, Alvarez Dorta D,
Sivignon A, Barnich N, Harduin-Lepers A, Larroulet I, Yanguas Serrano A,
Siriwardena A, Pesquera A, Zurutuza A, Gouin SG, Boukherroub R, Bouckaert J. 2016 Apr 1 ;5(2). pii : E14. doi : 10.3390/biology5020014.

The anti-adhesive strategy in Crohn’s disease : orally active mannosides to decolonize pathogenic Escherichia coli from the gut. Dimitri Alvarez Dorta, Adeline Sivignon, Thibaut Chalopin, Tetiana Dumych, Goedele Roos, Rostyslav Bilyy, David Deniaud, Eva-Maria Krammer, Jerome De Ruyck, Marc Lensink, Julie Bouckaert, Nicolas Barnich and Sébastien G. Gouin. ChemBioChem 2016. DOI : 10.1002/cbic.201600018

Structures of C-mannosylated anti-adhesives bound to the type 1 fimbrial FimH adhesin. Jerome de Ruyck, Marc F. Lensink and Julie Bouckaert. IUCr J 2016. DOI : 10.1107/S2052252516002487

Assessing Structural Predictions of Protein–Protein Recognition : The CAPRI Experiment. Abby L. Parrill and Kenny B. Lipkowitz, Joël Janin, Shoshana J. Wodak, Marc F. Lensink and Sameer Velankar. Reviews in Computational Chemistry Volume 28. 2016 DOI : 10.1002/9781118889886.ch4

Plasmonic photothermal cancer therapy with gold nanorods/reduced graphene oxide core/shell nanocomposites. Kostiantyn Turcheniuk, Tetiana Dumych, Rostyslav Bilyy, Volodymyr Turcheniuk, Julie Bouckaert, Volodymyr Vovk, Valentyna Chopyak, Vladimir Zaitzev, Pascal Mariot, Natacha Prevarskaya, Rabah Boukherroub, Sabine Szunerits. RSC Advances 2016 DOI : 10.1039/c5ra24662h.