Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 81

1.

Fitting Corrections to an RNA Force Field Using Experimental Data.

Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Šponer J, Bussi G.

J Chem Theory Comput. 2019 Jun 11;15(6):3425-3431. doi: 10.1021/acs.jctc.9b00206. Epub 2019 May 23.

PMID:
31050905
2.
3.

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models.

Pinamonti G, Paul F, Noé F, Rodriguez A, Bussi G.

J Chem Phys. 2019 Apr 21;150(15):154123. doi: 10.1063/1.5083227.

PMID:
31005065
4.

Water quality modelling of the Mekong River basin: Climate change and socioeconomics drive flow and nutrient flux changes to the Mekong Delta.

Whitehead PG, Jin L, Bussi G, Voepel HE, Darby SE, Vasilopoulos G, Manley R, Rodda H, Hutton C, Hackney C, Tri VPD, Hung NN.

Sci Total Environ. 2019 Jul 10;673:218-229. doi: 10.1016/j.scitotenv.2019.03.315. Epub 2019 Apr 6.

PMID:
30991313
5.

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P.

J Chem Theory Comput. 2019 May 14;15(5):3288-3305. doi: 10.1021/acs.jctc.8b00955. Epub 2019 Apr 2.

PMID:
30896943
6.

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting.

Rangan R, Bonomi M, Heller GT, Cesari A, Bussi G, Vendruscolo M.

J Chem Theory Comput. 2018 Dec 11;14(12):6632-6641. doi: 10.1021/acs.jctc.8b00738. Epub 2018 Nov 28.

PMID:
30428663
7.

Barnaba: software for analysis of nucleic acid structures and trajectories.

Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K.

RNA. 2019 Feb;25(2):219-231. doi: 10.1261/rna.067678.118. Epub 2018 Nov 12.

PMID:
30420522
8.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K.

Sci Adv. 2018 May 18;4(5):eaar8521. doi: 10.1126/sciadv.aar8521. eCollection 2018 May.

9.

Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops".

Bottaro S, Banáš P, Šponer J, Bussi G.

J Phys Chem Lett. 2018 Apr 5;9(7):1674-1675. doi: 10.1021/acs.jpclett.8b00754. Epub 2018 Mar 19. No abstract available.

PMID:
29553740
10.

Restoring water quality in the polluted Turag-Tongi-Balu river system, Dhaka: Modelling nutrient and total coliform intervention strategies.

Whitehead P, Bussi G, Hossain MA, Dolk M, Das P, Comber S, Peters R, Charles KJ, Hope R, Hossain MS.

Sci Total Environ. 2018 Aug 1;631-632:223-232. doi: 10.1016/j.scitotenv.2018.03.038. Epub 2018 Mar 16.

PMID:
29525703
11.

Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.

Podbevšek P, Fasolo F, Bon C, Cimatti L, Reißer S, Carninci P, Bussi G, Zucchelli S, Plavec J, Gustincich S.

Sci Rep. 2018 Feb 16;8(1):3189. doi: 10.1038/s41598-017-14908-6.

12.

Modelling the effects of climate and land-use change on the hydrochemistry and ecology of the River Wye (Wales).

Bussi G, Whitehead PG, Gutiérrez-Cánovas C, Ledesma JLJ, Ormerod SJ, Couture RM.

Sci Total Environ. 2018 Jun 15;627:733-743. doi: 10.1016/j.scitotenv.2018.01.295. Epub 2018 Feb 2.

PMID:
29426198
13.

Exploring RNA structure and dynamics through enhanced sampling simulations.

Mlýnský V, Bussi G.

Curr Opin Struct Biol. 2018 Apr;49:63-71. doi: 10.1016/j.sbi.2018.01.004. Epub 2018 Feb 4. Review.

PMID:
29414513
14.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M.

Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3.

15.

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

Poblete S, Bottaro S, Bussi G.

Nucleic Acids Res. 2018 Feb 28;46(4):1674-1683. doi: 10.1093/nar/gkx1269.

16.

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.

Mlýnský V, Bussi G.

J Phys Chem Lett. 2018 Jan 18;9(2):313-318. doi: 10.1021/acs.jpclett.7b02921. Epub 2018 Jan 4.

17.

Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.

Poblete S, Bottaro S, Bussi G.

Biochem Biophys Res Commun. 2018 Mar 29;498(2):352-358. doi: 10.1016/j.bbrc.2017.12.057. Epub 2017 Dec 14.

PMID:
29248728
18.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

Islam B, Stadlbauer P, Gil-Ley A, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banas P, Otyepka M, Sponer J.

J Chem Theory Comput. 2017 Jun 13;13(6):2458-2480. doi: 10.1021/acs.jctc.7b00226. Epub 2017 May 18.

19.

Modelling metaldehyde in catchments: a River Thames case-study.

Lu Q, Whitehead PG, Bussi G, Futter MN, Nizzetto L.

Environ Sci Process Impacts. 2017 Apr 19;19(4):586-595. doi: 10.1039/c6em00527f.

PMID:
28322378
20.

Dynamic response of land use and river nutrient concentration to long-term climatic changes.

Bussi G, Janes V, Whitehead PG, Dadson SJ, Holman IP.

Sci Total Environ. 2017 Jul 15;590-591:818-831. doi: 10.1016/j.scitotenv.2017.03.069. Epub 2017 Mar 10.

21.

Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.

Mlýnský V, Bussi G.

RNA. 2017 May;23(5):712-720. doi: 10.1261/rna.060442.116. Epub 2017 Feb 15.

22.

Unraveling Mg2+-RNA binding with atomistic molecular dynamics.

Cunha RA, Bussi G.

RNA. 2017 May;23(5):628-638. doi: 10.1261/rna.060079.116. Epub 2017 Feb 1.

23.

Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface.

Bellucci L, Bussi G, Di Felice R, Corni S.

Nanoscale. 2017 Feb 9;9(6):2279-2290. doi: 10.1039/c6nr06010b.

PMID:
28124697
24.

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.

Pinamonti G, Zhao J, Condon DE, Paul F, Noè F, Turner DH, Bussi G.

J Chem Theory Comput. 2017 Feb 14;13(2):926-934. doi: 10.1021/acs.jctc.6b00982. Epub 2017 Jan 5.

25.

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.

Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M.

Biochim Biophys Acta Gen Subj. 2017 May;1861(5 Pt B):1246-1263. doi: 10.1016/j.bbagen.2016.12.008. Epub 2016 Dec 13. Review.

PMID:
27979677
26.

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement.

Cesari A, Gil-Ley A, Bussi G.

J Chem Theory Comput. 2016 Dec 13;12(12):6192-6200. Epub 2016 Dec 5.

PMID:
27951677
27.

Free Energy Landscape of GAGA and UUCG RNA Tetraloops.

Bottaro S, Banáš P, Šponer J, Bussi G.

J Phys Chem Lett. 2016 Oct 20;7(20):4032-4038. Epub 2016 Sep 28. Erratum in: J Phys Chem Lett. 2018 Apr 5;9(7):1674-1675.

PMID:
27661094
28.

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P.

J Chem Theory Comput. 2016 Sep 13;12(9):4534-48. doi: 10.1021/acs.jctc.6b00300. Epub 2016 Aug 4.

29.

A theoretical assessment of microplastic transport in river catchments and their retention by soils and river sediments.

Nizzetto L, Bussi G, Futter MN, Butterfield D, Whitehead PG.

Environ Sci Process Impacts. 2016 Aug 10;18(8):1050-9. doi: 10.1039/c6em00206d.

PMID:
27255969
30.

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.

Gil-Ley A, Bottaro S, Bussi G.

J Chem Theory Comput. 2016 Jun 14;12(6):2790-8. doi: 10.1021/acs.jctc.6b00299. Epub 2016 May 16.

31.

RNA folding pathways in stop motion.

Bottaro S, Gil-Ley A, Bussi G.

Nucleic Acids Res. 2016 Jul 8;44(12):5883-91. doi: 10.1093/nar/gkw239. Epub 2016 Apr 18.

32.

Fate and transport of polychlorinated biphenyls (PCBs) in the River Thames catchment - Insights from a coupled multimedia fate and hydrobiogeochemical transport model.

Lu Q, Futter MN, Nizzetto L, Bussi G, Jürgens MD, Whitehead PG.

Sci Total Environ. 2016 Dec 1;572:1461-1470. doi: 10.1016/j.scitotenv.2016.03.029. Epub 2016 Apr 16.

PMID:
27090411
33.

Impacts of climate change, land-use change and phosphorus reduction on phytoplankton in the River Thames (UK).

Bussi G, Whitehead PG, Bowes MJ, Read DS, Prudhomme C, Dadson SJ.

Sci Total Environ. 2016 Dec 1;572:1507-1519. doi: 10.1016/j.scitotenv.2016.02.109. Epub 2016 Feb 28.

PMID:
26927961
34.

An INCA model for pathogens in rivers and catchments: Model structure, sensitivity analysis and application to the River Thames catchment, UK.

Whitehead PG, Leckie H, Rankinen K, Butterfield D, Futter MN, Bussi G.

Sci Total Environ. 2016 Dec 1;572:1601-1610. doi: 10.1016/j.scitotenv.2016.01.128. Epub 2016 Feb 11.

PMID:
26875602
35.

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Pérez-Villa A, Darvas M, Bussi G.

Nucleic Acids Res. 2016 Apr 7;44(6):2975. doi: 10.1093/nar/gkv1378. Epub 2015 Dec 3. No abstract available.

36.

Correction to Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

Gil-Ley A, Bussi G.

J Chem Theory Comput. 2015 Nov 10;11(11):5554. doi: 10.1021/acs.jctc.5b00981. Epub 2015 Oct 28. No abstract available.

37.

Accurate multiple time step in biased molecular simulations.

Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G.

J Chem Theory Comput. 2015 Jan 13;11(1):139-46. doi: 10.1021/ct5007086. Epub 2014 Dec 23.

PMID:
26574212
38.

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.

Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J.

Nucleic Acids Res. 2015 Nov 16;43(20):9626-44. doi: 10.1093/nar/gkv994. Epub 2015 Oct 3.

39.

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Pérez-Villa A, Darvas M, Bussi G.

Nucleic Acids Res. 2015 Oct 15;43(18):8725-34. doi: 10.1093/nar/gkv872. Epub 2015 Sep 10. Erratum in: Nucleic Acids Res. 2016 Apr 7;44(6):2975.

40.

Effects of afforestation on runoff and sediment load in an upland Mediterranean catchment.

Buendia C, Bussi G, Tuset J, Vericat D, Sabater S, Palau A, Batalla RJ.

Sci Total Environ. 2016 Jan 1;540:144-57. doi: 10.1016/j.scitotenv.2015.07.005. Epub 2015 Jul 15.

PMID:
26188652
41.

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

Pinamonti G, Bottaro S, Micheletti C, Bussi G.

Nucleic Acids Res. 2015 Sep 3;43(15):7260-9. doi: 10.1093/nar/gkv708. Epub 2015 Jul 17.

42.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

Di Palma F, Bottaro S, Bussi G.

BMC Bioinformatics. 2015;16 Suppl 9:S6. doi: 10.1186/1471-2105-16-S9-S6. Epub 2015 Jun 1.

43.
44.

Using reweighted pulling simulations to characterize conformational changes in riboswitches.

Di Palma F, Colizzi F, Bussi G.

Methods Enzymol. 2015;553:139-62. doi: 10.1016/bs.mie.2014.10.055. Epub 2015 Feb 3.

PMID:
25726464
45.

The role of nucleobase interactions in RNA structure and dynamics.

Bottaro S, Di Palma F, Bussi G.

Nucleic Acids Res. 2014 Dec 1;42(21):13306-14. doi: 10.1093/nar/gku972. Epub 2014 Oct 29.

46.

Bowl inversion of surface-adsorbed sumanene.

Jaafar R, Pignedoli CA, Bussi G, Aït-Mansour K, Groening O, Amaya T, Hirao T, Fasel R, Ruffieux P.

J Am Chem Soc. 2014 Oct 1;136(39):13666-71. doi: 10.1021/ja504126z. Epub 2014 Sep 18.

PMID:
25181621
47.

Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays.

Colizzi F, Lamontagne AM, Lafontaine DA, Bussi G.

Methods Mol Biol. 2014;1103:141-51. doi: 10.1007/978-1-62703-730-3_11.

PMID:
24318892
48.

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.

Di Palma F, Colizzi F, Bussi G.

RNA. 2013 Nov;19(11):1517-24. doi: 10.1261/rna.040493.113. Epub 2013 Sep 19.

49.

Structural role of uracil DNA glycosylase for the recognition of uracil in DNA duplexes. Clues from atomistic simulations.

Franco D, Sgrignani J, Bussi G, Magistrato A.

J Chem Inf Model. 2013 Jun 24;53(6):1371-87. doi: 10.1021/ci4001647. Epub 2013 Jun 11.

PMID:
23705837
50.

Surface enhanced Raman scattering, electronic spectrum and Mulliken charge distribution in the normal modes of bis(diethyldithiocarbamate)zinc(II) complex.

Téllez Soto CA, Costa AC Jr, Ramos JM, Versiane O, Ondar GF, Ferreira GB, Fávero PP, Rangel JL, Raniero L, Bueno Costa G, Bussi GG, Martin AA.

Spectrochim Acta A Mol Biomol Spectrosc. 2013 Jun;110:443-9. doi: 10.1016/j.saa.2013.03.039. Epub 2013 Mar 22.

PMID:
23588299

Supplemental Content

Support Center