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Items: 1 to 50 of 87

1.

Modulating Ligand Dissociation Through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers.

Estarellas C, Scaffidi S, Saladino G, Spyrakis F, Franzoni L, Galdeano C, Bidon-Chanal A, Gervasio FL, Luque FJ.

J Phys Chem Lett. 2019 Nov 12. doi: 10.1021/acs.jpclett.9b02861. [Epub ahead of print]

PMID:
31714784
2.

The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus.

Yalinca H, Gehin CJC, Oleinikovas V, Lashuel HA, Gervasio FL, Pastore A.

Front Mol Biosci. 2019 Oct 1;6:95. doi: 10.3389/fmolb.2019.00095. eCollection 2019.

3.

Editorial: Machine Learning in Biomolecular Simulations.

Verkhivker G, Spiwok V, Gervasio FL.

Front Mol Biosci. 2019 Aug 29;6:76. doi: 10.3389/fmolb.2019.00076. eCollection 2019. No abstract available.

4.

Understanding Ligand Binding Selectivity in a Prototypical GPCR Family.

Mattedi G, Deflorian F, Mason JS, de Graaf C, Gervasio FL.

J Chem Inf Model. 2019 Jun 24;59(6):2830-2836. doi: 10.1021/acs.jcim.9b00298. Epub 2019 Jun 4.

PMID:
31125224
5.

Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer.

Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL.

Cells. 2019 Apr 5;8(4). pii: E316. doi: 10.3390/cells8040316. Review.

6.

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor.

Kuzmanic A, Pritchard RB, Hansen DF, Gervasio FL.

J Phys Chem Lett. 2019 Apr 18;10(8):1928-1934. doi: 10.1021/acs.jpclett.9b00517. Epub 2019 Apr 8.

7.

Defining an Optimal Metric for the Path Collective Variables.

Hovan L, Comitani F, Gervasio FL.

J Chem Theory Comput. 2019 Jan 8;15(1):25-32. doi: 10.1021/acs.jctc.8b00563. Epub 2018 Dec 5.

PMID:
30468578
8.

The Structure of the Pro-domain of Mouse proNGF in Contact with the NGF Domain.

Yan R, Yalinca H, Paoletti F, Gobbo F, Marchetti L, Kuzmanic A, Lamba D, Gervasio FL, Konarev PV, Cattaneo A, Pastore A.

Structure. 2019 Jan 2;27(1):78-89.e3. doi: 10.1016/j.str.2018.09.013. Epub 2018 Nov 1.

PMID:
30393051
9.

The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers.

Zanetti-Domingues LC, Korovesis D, Needham SR, Tynan CJ, Sagawa S, Roberts SK, Kuzmanic A, Ortiz-Zapater E, Jain P, Roovers RC, Lajevardipour A, van Bergen En Henegouwen PMP, Santis G, Clayton AHA, Clarke DT, Gervasio FL, Shan Y, Shaw DE, Rolfe DJ, Parker PJ, Martin-Fernandez ML.

Nat Commun. 2018 Oct 18;9(1):4325. doi: 10.1038/s41467-018-06632-0.

10.

A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics.

Haldar S, Comitani F, Saladino G, Woods C, van der Kamp MW, Mulholland AJ, Gervasio FL.

J Chem Theory Comput. 2018 Nov 13;14(11):6093-6101. doi: 10.1021/acs.jctc.8b00687. Epub 2018 Oct 2.

PMID:
30208708
11.

Role of glutamine synthetase in angiogenesis beyond glutamine synthesis.

Eelen G, Dubois C, Cantelmo AR, Goveia J, Brüning U, DeRan M, Jarugumilli G, van Rijssel J, Saladino G, Comitani F, Zecchin A, Rocha S, Chen R, Huang H, Vandekeere S, Kalucka J, Lange C, Morales-Rodriguez F, Cruys B, Treps L, Ramer L, Vinckier S, Brepoels K, Wyns S, Souffreau J, Schoonjans L, Lamers WH, Wu Y, Haustraete J, Hofkens J, Liekens S, Cubbon R, Ghesquière B, Dewerchin M, Gervasio FL, Li X, van Buul JD, Wu X, Carmeliet P.

Nature. 2018 Sep;561(7721):63-69. doi: 10.1038/s41586-018-0466-7. Epub 2018 Aug 29.

12.

Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance.

Galdadas I, Lovera S, Pérez-Hernández G, Barnes MD, Healy J, Afsharikho H, Woodford N, Bonomo RA, Gervasio FL, Haider S.

Sci Rep. 2018 Aug 27;8(1):12916. doi: 10.1038/s41598-018-31176-0.

13.

Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases.

Ordan M, Pallara C, Maik-Rachline G, Hanoch T, Gervasio FL, Glaser F, Fernandez-Recio J, Seger R.

Sci Rep. 2018 Aug 7;8(1):11830. doi: 10.1038/s41598-018-30202-5.

14.

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH.

Comitani F, Gervasio FL.

J Chem Theory Comput. 2018 Jun 12;14(6):3321-3331. doi: 10.1021/acs.jctc.8b00263. Epub 2018 May 25.

PMID:
29768914
15.

Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells.

Tsuchiya Y, Zhyvoloup A, Baković J, Thomas N, Yu BYK, Das S, Orengo C, Newell C, Ward J, Saladino G, Comitani F, Gervasio FL, Malanchuk OM, Khoruzhenko AI, Filonenko V, Peak-Chew SY, Skehel M, Gout I.

Biochem J. 2018 Jun 6;475(11):1909-1937. doi: 10.1042/BCJ20180043.

16.

Assessment of the model refinement category in CASP12.

Hovan L, Oleinikovas V, Yalinca H, Kryshtafovych A, Saladino G, Gervasio FL.

Proteins. 2018 Mar;86 Suppl 1:152-167. doi: 10.1002/prot.25409. Epub 2017 Nov 29.

PMID:
29071750
17.

Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations.

Saleh N, Saladino G, Gervasio FL, Clark T.

Chem Sci. 2017 May 1;8(5):4019-4026. doi: 10.1039/c6sc04647a. Epub 2017 Mar 24.

18.

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands.

Saleh N, Ibrahim P, Saladino G, Gervasio FL, Clark T.

J Chem Inf Model. 2017 May 22;57(5):1210-1217. doi: 10.1021/acs.jcim.6b00772. Epub 2017 May 8.

PMID:
28453271
19.

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations.

Kuzmanic A, Sutto L, Saladino G, Nebreda AR, Gervasio FL, Orozco M.

Elife. 2017 Apr 26;6. pii: e22175. doi: 10.7554/eLife.22175.

20.

Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET.

Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PM, Chin JW, Gervasio FL, Tate EW, Katan M.

Sci Rep. 2017 Jan 3;7:39841. doi: 10.1038/srep39841.

21.

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations.

Oleinikovas V, Saladino G, Cossins BP, Gervasio FL.

J Am Chem Soc. 2016 Nov 2;138(43):14257-14263. Epub 2016 Oct 20.

22.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.

Lambrughi M, De Gioia L, Gervasio FL, Lindorff-Larsen K, Nussinov R, Urani C, Bruschi M, Papaleo E.

Nucleic Acids Res. 2016 Nov 2;44(19):9096-9109. Epub 2016 Sep 6.

23.

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.

Schulze JO, Saladino G, Busschots K, Neimanis S, Süß E, Odadzic D, Zeuzem S, Hindie V, Herbrand AK, Lisa MN, Alzari PM, Gervasio FL, Biondi RM.

Cell Chem Biol. 2016 Oct 20;23(10):1193-1205. doi: 10.1016/j.chembiol.2016.06.017. Epub 2016 Sep 29.

24.

Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling.

Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F.

Cancer Cell. 2016 Jul 11;30(1):176-178. doi: 10.1016/j.ccell.2016.06.015. Epub 2016 Jul 11. No abstract available.

25.

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome.

Pucheta-Martinez E, D'Amelio N, Lelli M, Martinez-Torrecuadrada JL, Sudol M, Saladino G, Gervasio FL.

Sci Rep. 2016 Jul 26;6:30293. doi: 10.1038/srep30293.

26.

A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors.

Saleh N, Saladino G, Gervasio FL, Haensele E, Banting L, Whitley DC, Sopkova-de Oliveira Santos J, Bureau R, Clark T.

Angew Chem Int Ed Engl. 2016 Jul 4;55(28):8008-12. doi: 10.1002/anie.201602729. Epub 2016 May 17.

PMID:
27184628
27.

Molecular engineering of polymersome surface topology.

Ruiz-Pérez L, Messager L, Gaitzsch J, Joseph A, Sutto L, Gervasio FL, Battaglia G.

Sci Adv. 2016 Apr 15;2(4):e1500948. doi: 10.1126/sciadv.1500948. eCollection 2016 Apr.

28.

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, van den Broek K, Epple M, Kuhn H, Truszkowski A, Zielesny A, Fraaije JH, Gracia RS, Kast SM, Bulusu KC, Bender A, Yosipof A, Nahum O, Senderowitz H, Krotzky T, Schulz R, Wolber G, Bietz S, Rarey M, Zimmermann MO, Lange A, Ruff M, Heidrich J, Onlia I, Exner TE, Boeckler FM, Bermudez M, Firaha DS, Hollóczki O, Kirchner B, Tautermann CS, Volkamer A, Eid S, Turk S, Rippmann F, Fulle S, Saleh N, Saladino G, Gervasio FL, Haensele E, Banting L, Whitley DC, Oliveira Santos JS, Bureau R, Clark T, Sandmann A, Lanig H, Kibies P, Heil J, Hoffgaard F, Frach R, Engel J, Smith S, Basu D, Rauh D, Kohlbacher O, Boeckler FM, Essex JW, Bodnarchuk MS, Ross GA, Finkelmann AR, Göller AH, Schneider G, Husch T, Schütter C, Balducci A, Korth M, Ntie-Kang F, Günther S, Sippl W, Mbaze LM, Ntie-Kang F, Simoben CV, Lifongo LL, Ntie-Kang F, Judson P, Barilla J, Lokajíček MV, Pisaková H, Simr P, Kireeva N, Petrov A, Ostroumov D, Solovev VP, Pervov VS, Friedrich NO, Sommer K, Rarey M, Kirchmair J, Proschak E, Weber J, Moser D, Kalinowski L, Achenbach J, Mackey M, Cheeseright T, Renner G, Renner G, Schmidt TC, Schram J, Egelkraut-Holtus M, van Oeyen A, Kalliokoski T, Fourches D, Ibezim A, Mbah CJ, Adikwu UM, Nwodo NJ, Steudle A, Masek BB, Nagy S, Baker D, Soltanshahi F, Dorfman R, Dubrucq K, Patel H, Koch O, Mrugalla F, Kast SM, Ain QU, Fuchs JE, Owen RM, Omoto K, Torella R, Pryde DC, Glen R, Bender A, Hošek P, Spiwok V, Mervin LH, Barrett I, Firth M, Murray DC, McWilliams L, Cao Q, Engkvist O, Warszycki D, Śmieja M, Bojarski AJ, Aniceto N, Freitas A, Ghafourian T, Herrmann G, Eigner-Pitto V, Naß A, Kurczab R, Bojarski AJ, Lange A, Günther MB, Hennig S, Büttner FM, Schall C, Sievers-Engler A, Ansideri F, Koch P, Stehle T, Laufer S, Böckler FM, Zdrazil B, Montanari F, Ecker GF, Grebner C, Hogner A, Ulander J, Edman K, Guallar V, Tyrchan C, Ulander J, Tyrchan C, Klute W, Bergström F, Kramer C, Nguyen QD, Frach R, Kibies P, Strohfeldt S, Böttcher S, Pongratz T, Horinek D, Kast SM, Rupp B, Al-Yamori R, Lisurek M, Kühne R, Furtado F, van den Broek K, Wessjohann L, Mathea M, Baumann K, Mohamad-Zobir SZ, Fu X, Fan TP, Bender A, Kuhn MA, Sotriffer CA, Zoufir A, Li X, Mervin L, Berg E, Polokoff M, Ihlenfeldt WD, Ihlenfeldt WD, Pretzel J, Alhalabi Z, Fraczkiewicz R, Waldman M, Clark RD, Shaikh N, Garg P, Kos A, Himmler HJ, Sandmann A, Jardin C, Sticht H, Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W, Pöhner IA, Panecka J, Wade RC, Bietz S, Schomburg KT, Hilbig M, Rarey M, Jäger C, Wieczorek V, Westerhoff LM, Borbulevych OY, Demuth HU, Buchholz M, Schmidt D, Rickmeyer T, Krotzky T, Kolb P, Mittal S, Sánchez-García E, Nogueira MS, Oliveira TB, da Costa FB, Schmidt TJ.

J Cheminform. 2016 Apr 26;8(Suppl 1):18. doi: 10.1186/s13321-016-0119-5. No abstract available.

29.

Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.

Morando MA, Saladino G, D'Amelio N, Pucheta-Martinez E, Lovera S, Lelli M, López-Méndez B, Marenchino M, Campos-Olivas R, Gervasio FL.

Sci Rep. 2016 Apr 18;6:24439. doi: 10.1038/srep24439.

30.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase.

Pucheta-Martínez E, Saladino G, Morando MA, Martinez-Torrecuadrada J, Lelli M, Sutto L, D'Amelio N, Gervasio FL.

Sci Rep. 2016 Apr 11;6:24235. doi: 10.1038/srep24235.

31.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R.

Chem Rev. 2016 Jun 8;116(11):6391-423. doi: 10.1021/acs.chemrev.5b00623. Epub 2016 Feb 18. Review.

PMID:
26889708
32.

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases.

Saladino G, Gervasio FL.

Curr Opin Struct Biol. 2016 Apr;37:108-14. doi: 10.1016/j.sbi.2016.01.005. Epub 2016 Jan 26. Review.

PMID:
26820051
33.

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics.

Lovera S, Morando M, Pucheta-Martinez E, Martinez-Torrecuadrada JL, Saladino G, Gervasio FL.

PLoS Comput Biol. 2015 Nov 25;11(11):e1004578. doi: 10.1371/journal.pcbi.1004578. eCollection 2015 Nov.

34.

New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations.

Doro F, Saladino G, Belvisi L, Civera M, Gervasio FL.

J Chem Theory Comput. 2015 Apr 14;11(4):1354-9. doi: 10.1021/ct5010164.

PMID:
26574347
35.

From residue coevolution to protein conformational ensembles and functional dynamics.

Sutto L, Marsili S, Valencia A, Gervasio FL.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13567-72. doi: 10.1073/pnas.1508584112. Epub 2015 Oct 20.

36.

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study.

Bunney TD, Wan S, Thiyagarajan N, Sutto L, Williams SV, Ashford P, Koss H, Knowles MA, Gervasio FL, Coveney PV, Katan M.

EBioMedicine. 2015 Mar 1;2(3):194-204.

37.

The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase.

Marino KA, Sutto L, Gervasio FL.

J Am Chem Soc. 2015 Apr 29;137(16):5280-3. doi: 10.1021/jacs.5b01421. Epub 2015 Apr 17.

PMID:
25868080
38.

Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.

Cavalli A, Spitaleri A, Saladino G, Gervasio FL.

Acc Chem Res. 2015 Feb 17;48(2):277-85. doi: 10.1021/ar500356n. Epub 2014 Dec 12. Review.

PMID:
25496113
39.

The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion.

Dölker N, Górna MW, Sutto L, Torralba AS, Superti-Furga G, Gervasio FL.

PLoS Comput Biol. 2014 Oct 9;10(10):e1003863. doi: 10.1371/journal.pcbi.1003863. eCollection 2014 Oct.

40.

Conformational Changes and Free Energies in a Proline Isomerase.

Papaleo E, Sutto L, Gervasio FL, Lindorff-Larsen K.

J Chem Theory Comput. 2014 Sep 9;10(9):4169-74. doi: 10.1021/ct500536r.

PMID:
26588555
41.

Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes.

Goñi GM, Epifano C, Boskovic J, Camacho-Artacho M, Zhou J, Bronowska A, Martín MT, Eck MJ, Kremer L, Gräter F, Gervasio FL, Perez-Moreno M, Lietha D.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):E3177-86. doi: 10.1073/pnas.1317022111. Epub 2014 Jul 21.

42.

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase.

Sutto L, Gervasio FL.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10616-21. doi: 10.1073/pnas.1221953110. Epub 2013 Jun 10.

43.

Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling.

Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F.

Cancer Cell. 2013 Apr 15;23(4):489-501. doi: 10.1016/j.ccr.2013.02.018. Erratum in: Cancer Cell. 2016 Jul 11;30(1):176-178.

44.

Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties.

Bono F, De Smet F, Herbert C, De Bock K, Georgiadou M, Fons P, Tjwa M, Alcouffe C, Ny A, Bianciotto M, Jonckx B, Murakami M, Lanahan AA, Michielsen C, Sibrac D, Dol-Gleizes F, Mazzone M, Zacchigna S, Herault JP, Fischer C, Rigon P, Ruiz de Almodovar C, Claes F, Blanc I, Poesen K, Zhang J, Segura I, Gueguen G, Bordes MF, Lambrechts D, Broussy R, van de Wouwer M, Michaux C, Shimada T, Jean I, Blacher S, Noel A, Motte P, Rom E, Rakic JM, Katsuma S, Schaeffer P, Yayon A, Van Schepdael A, Schwalbe H, Gervasio FL, Carmeliet G, Rozensky J, Dewerchin M, Simons M, Christopoulos A, Herbert JM, Carmeliet P.

Cancer Cell. 2013 Apr 15;23(4):477-88. doi: 10.1016/j.ccr.2013.02.019.

45.

Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.

Juraszek J, Saladino G, van Erp TS, Gervasio FL.

Phys Rev Lett. 2013 Mar 8;110(10):108106. Epub 2013 Mar 8.

PMID:
23521305
46.

The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor.

Sahún-Roncero M, Rubio-Ruiz B, Saladino G, Conejo-García A, Espinosa A, Velázquez-Campoy A, Gervasio FL, Entrena A, Hurtado-Guerrero R.

Angew Chem Int Ed Engl. 2013 Apr 22;52(17):4582-6. doi: 10.1002/anie.201209660. Epub 2013 Feb 25.

PMID:
23441033
47.

New insights in protein kinase conformational dynamics.

Saladino G, Gervasio FL.

Curr Top Med Chem. 2012;12(17):1889-95. Review.

PMID:
23116468
48.

Non-specific protein-DNA interactions control I-CreI target binding and cleavage.

Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Epinat JC, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G.

Nucleic Acids Res. 2012 Aug;40(14):6936-45. doi: 10.1093/nar/gks320. Epub 2012 Apr 11.

49.

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors.

Saladino G, Gauthier L, Bianciotto M, Gervasio FL.

J Chem Theory Comput. 2012 Apr 10;8(4):1165-70. doi: 10.1021/ct3001377. Epub 2012 Mar 29.

PMID:
26596735
50.

The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation.

Lovera S, Sutto L, Boubeva R, Scapozza L, Dölker N, Gervasio FL.

J Am Chem Soc. 2012 Feb 8;134(5):2496-9. doi: 10.1021/ja210751t. Epub 2012 Jan 30.

PMID:
22280319

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