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Items: 1 to 50 of 101

1.

Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its Cα Carbons.

Sormani G, Rodriguez A, Laio A.

J Chem Theory Comput. 2020 Jan 14;16(1):80-87. doi: 10.1021/acs.jctc.9b00800. Epub 2019 Dec 20.

PMID:
31809040
2.

A common root for coevolution and substitution rate variability in protein sequence evolution.

Rizzato F, Zamuner S, Pagnani A, Laio A.

Sci Rep. 2019 Dec 2;9(1):18032. doi: 10.1038/s41598-019-53958-w.

3.

A consensus protocol for the in silico optimisation of antibody fragments.

Soler MA, Medagli B, Semrau MS, Storici P, Bajc G, de Marco A, Laio A, Fortuna S.

Chem Commun (Camb). 2019 Nov 19;55(93):14043-14046. doi: 10.1039/c9cc06182g.

PMID:
31690899
4.

Spontaneously Forming Dendritic Voids in Liquid Water Can Host Small Polymers.

Ansari N, Laio A, Hassanali A.

J Phys Chem Lett. 2019 Sep 19;10(18):5585-5591. doi: 10.1021/acs.jpclett.9b02052. Epub 2019 Sep 6.

PMID:
31469575
5.

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations.

Ochoa R, Laio A, Cossio P.

J Chem Inf Model. 2019 Aug 26;59(8):3464-3473. doi: 10.1021/acs.jcim.9b00403. Epub 2019 Jul 23.

PMID:
31290667
6.

The intrinsic dimension of protein sequence evolution.

Facco E, Pagnani A, Russo ET, Laio A.

PLoS Comput Biol. 2019 Apr 8;15(4):e1006767. doi: 10.1371/journal.pcbi.1006767. eCollection 2019 Apr.

7.

The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions.

Marchetti F, Capelli R, Rizzato F, Laio A, Colombo G.

J Phys Chem Lett. 2019 Apr 4;10(7):1489-1497. doi: 10.1021/acs.jpclett.9b00191. Epub 2019 Mar 18.

PMID:
30855965
8.

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids.

Ochoa R, Soler MA, Laio A, Cossio P.

Phys Chem Chem Phys. 2018 Oct 17;20(40):25901-25909. doi: 10.1039/c8cp03826k.

PMID:
30289133
9.

Preface: Special Topic on Enhanced Sampling for Molecular Systems.

Laio A, Panagiotopoulos AZ, Zuckerman DM.

J Chem Phys. 2018 Aug 21;149(7):072001. doi: 10.1063/1.5049669.

PMID:
30134673
10.

The permeation mechanism of organic cations through a CNG mimic channel.

Napolitano LMR, Marchesi A, Rodriguez A, De March M, Onesti S, Laio A, Torre V.

PLoS Comput Biol. 2018 Aug 2;14(8):e1006295. doi: 10.1371/journal.pcbi.1006295. eCollection 2018 Aug.

11.

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition.

Battisti A, Zamuner S, Sarti E, Laio A.

Phys Chem Chem Phys. 2018 Jun 27;20(25):17148-17155. doi: 10.1039/c7cp08170g.

PMID:
29900428
12.

Computing the Free Energy without Collective Variables.

Rodriguez A, d'Errico M, Facco E, Laio A.

J Chem Theory Comput. 2018 Mar 13;14(3):1206-1215. doi: 10.1021/acs.jctc.7b00916. Epub 2018 Feb 19.

PMID:
29401379
13.

Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories.

Soler MA, Fortuna S, de Marco A, Laio A.

Phys Chem Chem Phys. 2018 Jan 31;20(5):3438-3444. doi: 10.1039/c7cp08116b.

PMID:
29328338
14.

Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes.

Škrbić T, Zamuner S, Hong R, Seno F, Laio A, Trovato A.

Proteins. 2018 Apr;86(4):393-404. doi: 10.1002/prot.25454. Epub 2018 Jan 21.

PMID:
29318668
15.

A Markov state modeling analysis of sliding dynamics of a 2D model.

Teruzzi M, Pellegrini F, Laio A, Tosatti E.

J Chem Phys. 2017 Oct 21;147(15):152721. doi: 10.1063/1.4986458.

PMID:
29055312
16.

Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment.

Guida F, Battisti A, Gladich I, Buzzo M, Marangon E, Giodini L, Toffoli G, Laio A, Berti F.

Biosens Bioelectron. 2018 Feb 15;100:298-303. doi: 10.1016/j.bios.2017.09.012. Epub 2017 Sep 14.

PMID:
28942212
17.

Estimating the intrinsic dimension of datasets by a minimal neighborhood information.

Facco E, d'Errico M, Rodriguez A, Laio A.

Sci Rep. 2017 Sep 22;7(1):12140. doi: 10.1038/s41598-017-11873-y.

18.

New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods.

Maity S, Ilieva N, Laio A, Torre V, Mazzolini M.

Sci Rep. 2017 Sep 20;7(1):12000. doi: 10.1038/s41598-017-11912-8.

19.

Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms.

Rizzato F, Rodriguez A, Biarnés X, Laio A.

Genetics. 2017 Oct;207(2):643-652. doi: 10.1534/genetics.117.300078. Epub 2017 Jul 28.

20.

Computational design of cyclic peptides for the customized oriented immobilization of globular proteins.

Soler MA, Rodriguez A, Russo A, Adedeji AF, Dongmo Foumthuim CJ, Cantarutti C, Ambrosetti E, Casalis L, Corazza A, Scoles G, Marasco D, Laio A, Fortuna S.

Phys Chem Chem Phys. 2017 Jan 25;19(4):2740-2748. doi: 10.1039/c6cp07807a.

PMID:
28059415
21.

Markov state modeling of sliding friction.

Pellegrini F, Landes FP, Laio A, Prestipino S, Tosatti E.

Phys Rev E. 2016 Nov;94(5-1):053001. Epub 2016 Nov 2.

PMID:
27967165
22.

fMRI single trial discovery of spatio-temporal brain activity patterns.

Allegra M, Seyed-Allaei S, Pizzagalli F, Baftizadeh F, Maieron M, Reverberi C, Laio A, Amati D.

Hum Brain Mapp. 2017 Mar;38(3):1421-1437. doi: 10.1002/hbm.23463. Epub 2016 Nov 23.

PMID:
27879036
23.

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

Rosa M, Micciarelli M, Laio A, Baroni S.

J Chem Theory Comput. 2016 Sep 13;12(9):4385-9. doi: 10.1021/acs.jctc.6b00470. Epub 2016 Aug 26.

PMID:
27494227
24.

Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations.

Ghaemi Z, Alberga D, Carloni P, Laio A, Lattanzi G.

J Chem Theory Comput. 2016 Aug 9;12(8):4093-9. doi: 10.1021/acs.jctc.5b01126. Epub 2016 Jul 20.

PMID:
27392273
25.

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates.

Rizzato F, Rodriguez A, Laio A.

BMC Bioinformatics. 2016 Jun 24;17:258. doi: 10.1186/s12859-016-1135-1.

26.

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide.

Lousa D, Pinto AR, Victor BL, Laio A, Veiga AS, Castanho MA, Soares CM.

Sci Rep. 2016 Jun 15;6:28099. doi: 10.1038/srep28099.

27.

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

Sarti E, Gladich I, Zamuner S, Correia BE, Laio A.

Proteins. 2016 Sep;84(9):1312-20. doi: 10.1002/prot.25079. Epub 2016 Jun 23.

PMID:
27253756
28.

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4.

Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M.

J Chem Theory Comput. 2016 Apr 12;12(4):2101-9. doi: 10.1021/acs.jctc.6b00075. Epub 2016 Mar 23.

PMID:
26967371
29.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Granata D, Baftizadeh F, Habchi J, Galvagnion C, De Simone A, Camilloni C, Laio A, Vendruscolo M.

Sci Rep. 2015 Oct 26;5:15449. doi: 10.1038/srep15449.

30.

Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

Gladich I, Rodriguez A, Hong Enriquez RP, Guida F, Berti F, Laio A.

J Phys Chem B. 2015 Oct 15;119(41):12963-9. doi: 10.1021/acs.jpcb.5b06227. Epub 2015 Oct 1.

PMID:
26398715
31.

A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels.

Napolitano LM, Bisha I, De March M, Marchesi A, Arcangeletti M, Demitri N, Mazzolini M, Rodriguez A, Magistrato A, Onesti S, Laio A, Torre V.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3619-28. doi: 10.1073/pnas.1503334112. Epub 2015 Jun 22.

32.

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P.

Chem Rev. 2015 May 13;115(9):3518-63. doi: 10.1021/cr500638n. Epub 2015 Mar 19. Review. No abstract available.

33.

Native fold and docking pose discrimination by the same residue-based scoring function.

Sarti E, Granata D, Seno F, Trovato A, Laio A.

Proteins. 2015 Apr;83(4):621-30. doi: 10.1002/prot.24764. Epub 2015 Feb 5.

PMID:
25619680
34.

Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT.

Bisha I, Rodriguez A, Laio A, Magistrato A.

PLoS Comput Biol. 2014 Dec 18;10(12):e1004017. doi: 10.1371/journal.pcbi.1004017. eCollection 2014 Dec.

35.

Machine learning. Clustering by fast search and find of density peaks.

Rodriguez A, Laio A.

Science. 2014 Jun 27;344(6191):1492-6. doi: 10.1126/science.1242072.

PMID:
24970081
36.

Shape and area fluctuation effects on nucleation theory.

Prestipino S, Laio A, Tosatti E.

J Chem Phys. 2014 Mar 7;140(9):094501. doi: 10.1063/1.4866971.

PMID:
24606362
37.

Nucleation process of a fibril precursor in the C-terminal segment of amyloid-β.

Baftizadeh F, Pietrucci F, Biarnés X, Laio A.

Phys Rev Lett. 2013 Apr 19;110(16):168103. Epub 2013 Apr 17.

PMID:
23679641
38.

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.

Granata D, Camilloni C, Vendruscolo M, Laio A.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6817-22. doi: 10.1073/pnas.1218350110. Epub 2013 Apr 9.

39.

A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation.

Prestipino S, Laio A, Tosatti E.

J Chem Phys. 2013 Feb 14;138(6):064508. doi: 10.1063/1.4790635.

PMID:
23425480
40.

A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations.

Bisha I, Laio A, Magistrato A, Giorgetti A, Sgrignani J.

J Chem Theory Comput. 2013 Feb 12;9(2):1240-6. doi: 10.1021/ct3008233. Epub 2013 Jan 16.

PMID:
26588767
41.

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation.

Hu XL, Piccinin S, Laio A, Fabris S.

ACS Nano. 2012 Dec 21;6(12):10497-504. doi: 10.1021/nn3044325. Epub 2012 Nov 20.

PMID:
23145574
42.

Absolute transition rates for rare events from dynamical decoupling of reaction variables.

Gobbo G, Laio A, Maleki A, Baroni S.

Phys Rev Lett. 2012 Oct 12;109(15):150601. Epub 2012 Oct 12.

PMID:
23102289
43.

Systematic improvement of classical nucleation theory.

Prestipino S, Laio A, Tosatti E.

Phys Rev Lett. 2012 Jun 1;108(22):225701. Epub 2012 May 30.

PMID:
23003623
44.

A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations.

Ghaemi Z, Minozzi M, Carloni P, Laio A.

J Phys Chem B. 2012 Jul 26;116(29):8714-21. doi: 10.1021/jp301083h. Epub 2012 May 10.

PMID:
22540377
45.

Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach.

Hong Enriquez RP, Pavan S, Benedetti F, Tossi A, Savoini A, Berti F, Laio A.

J Chem Theory Comput. 2012 Mar 13;8(3):1121-8. doi: 10.1021/ct200873y. Epub 2012 Feb 28.

PMID:
26593371
46.

Multidimensional view of amyloid fibril nucleation in atomistic detail.

Baftizadeh F, Biarnes X, Pietrucci F, Affinito F, Laio A.

J Am Chem Soc. 2012 Feb 29;134(8):3886-94. doi: 10.1021/ja210826a. Epub 2012 Feb 16.

PMID:
22276669
47.

Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations.

Rossetti G, Cossio P, Laio A, Carloni P.

FEBS Lett. 2011 Oct 3;585(19):3086-9. doi: 10.1016/j.febslet.2011.08.036. Epub 2011 Aug 30.

48.

Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions.

Cardamone L, Laio A, Torre V, Shahapure R, DeSimone A.

Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):13978-83. doi: 10.1073/pnas.1100549108. Epub 2011 Aug 8.

49.

Initial stages of salt crystal dissolution determined with ab initio molecular dynamics.

Liu LM, Laio A, Michaelides A.

Phys Chem Chem Phys. 2011 Aug 7;13(29):13162-6. doi: 10.1039/c1cp21077g. Epub 2011 Jun 2.

PMID:
21637872
50.

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Cossio P, Laio A, Pietrucci F.

Phys Chem Chem Phys. 2011 Jun 14;13(22):10421-5. doi: 10.1039/c0cp02675a. Epub 2011 Apr 4.

PMID:
21465020

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