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Items: 1 to 50 of 121

1.

Machine learning for protein folding and dynamics.

Noé F, De Fabritiis G, Clementi C.

Curr Opin Struct Biol. 2019 Dec 24;60:77-84. doi: 10.1016/j.sbi.2019.12.005. [Epub ahead of print] Review.

PMID:
31881449
2.

Nanoscale coupling of endocytic pit growth and stability.

Lehmann M, Lukonin I, Noé F, Schmoranzer J, Clementi C, Loerke D, Haucke V.

Sci Adv. 2019 Nov 27;5(11):eaax5775. doi: 10.1126/sciadv.aax5775. eCollection 2019 Nov.

3.

Coarse-graining molecular systems by spectral matching.

Nüske F, Boninsegna L, Clementi C.

J Chem Phys. 2019 Jul 28;151(4):044116. doi: 10.1063/1.5100131.

PMID:
31370528
4.

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields.

Wang J, Olsson S, Wehmeyer C, Pérez A, Charron NE, de Fabritiis G, Noé F, Clementi C.

ACS Cent Sci. 2019 May 22;5(5):755-767. doi: 10.1021/acscentsci.8b00913. Epub 2019 Apr 15.

5.

Localizing Frustration in Proteins Using All-Atom Energy Functions.

Chen J, Schafer NP, Wolynes PG, Clementi C.

J Phys Chem B. 2019 May 30;123(21):4497-4504. doi: 10.1021/acs.jpcb.9b01545. Epub 2019 May 16.

6.

Transient absorption spectroscopic studies on 4-nitroquinoline N-oxide: From femtoseconds to microseconds timescale.

Duran-Giner N, Carlotti B, Clementi C, Elisei F, Encinas S, Miranda MA.

Spectrochim Acta A Mol Biomol Spectrosc. 2019 Jun 5;216:265-272. doi: 10.1016/j.saa.2019.02.105. Epub 2019 Feb 27.

PMID:
30904634
7.

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.

Abella JR, Antunes DA, Clementi C, Kavraki LE.

Molecules. 2019 Mar 2;24(5). pii: E881. doi: 10.3390/molecules24050881.

8.

Effect of hydrogen bonding interaction on the photophysics of α-amino-orcein.

Clementi C, Carlotti B, Burattini C, Pellegrino RM, Romani A, Elisei F.

Spectrochim Acta A Mol Biomol Spectrosc. 2019 May 5;214:522-530. doi: 10.1016/j.saa.2019.02.057. Epub 2019 Feb 19.

PMID:
30818151
9.

Onion (Allium cepa L.) Skin: A Rich Resource of Biomolecules for the Sustainable Production of Colored Biofunctional Textiles.

Pucciarini L, Ianni F, Petesse V, Pellati F, Brighenti V, Volpi C, Gargaro M, Natalini B, Clementi C, Sardella R.

Molecules. 2019 Feb 11;24(3). pii: E634. doi: 10.3390/molecules24030634.

10.

Quantitative comparison of adaptive sampling methods for protein dynamics.

Hruska E, Abella JR, Nüske F, Kavraki LE, Clementi C.

J Chem Phys. 2018 Dec 28;149(24):244119. doi: 10.1063/1.5053582.

PMID:
30599712
11.

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T.

J Chem Phys. 2018 Nov 14;149(18):180901. doi: 10.1063/1.5052551.

PMID:
30441927
12.

The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family.

Yrazu FM, Pinamonti G, Clementi C.

J Phys Chem B. 2018 Dec 13;122(49):11800-11806. doi: 10.1021/acs.jpcb.8b08676. Epub 2018 Oct 16.

PMID:
30277393
13.

Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex.

Pinamonti G, Campo G, Chen J, Kluber A, Clementi C.

Biophys J. 2018 Oct 16;115(8):1470-1480. doi: 10.1016/j.bpj.2018.08.043. Epub 2018 Sep 7.

14.

Size and topology modulate the effects of frustration in protein folding.

Kluber A, Burt TA, Clementi C.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):9234-9239. doi: 10.1073/pnas.1801406115. Epub 2018 Aug 27.

15.

Sparse learning of stochastic dynamical equations.

Boninsegna L, Nüske F, Clementi C.

J Chem Phys. 2018 Jun 28;148(24):241723. doi: 10.1063/1.5018409.

PMID:
29960307
16.

Learning Effective Molecular Models from Experimental Observables.

Chen J, Chen J, Pinamonti G, Clementi C.

J Chem Theory Comput. 2018 Jul 10;14(7):3849-3858. doi: 10.1021/acs.jctc.8b00187. Epub 2018 Jun 13.

PMID:
29806937
17.

Rapid Calculation of Molecular Kinetics Using Compressed Sensing.

Litzinger F, Boninsegna L, Wu H, Nüske F, Patel R, Baraniuk R, Noé F, Clementi C.

J Chem Theory Comput. 2018 May 8;14(5):2771-2783. doi: 10.1021/acs.jctc.8b00089. Epub 2018 Apr 24.

PMID:
29660273
18.

Comparison of Tagging Technologies for Safeguards of Copper Canisters for Nuclear Spent Fuel.

Clementi C, Littmann F, Capineri L.

Sensors (Basel). 2018 Mar 21;18(4). pii: E929. doi: 10.3390/s18040929. Review.

19.

A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures.

Boninsegna L, Banisch R, Clementi C.

J Chem Theory Comput. 2018 Jan 9;14(1):453-460. doi: 10.1021/acs.jctc.7b00990. Epub 2017 Dec 22.

PMID:
29207235
20.

H3K27me3 dynamics dictate evolving uterine states in pregnancy and parturition.

Nancy P, Siewiera J, Rizzuto G, Tagliani E, Osokine I, Manandhar P, Dolgalev I, Clementi C, Tsirigos A, Erlebacher A.

J Clin Invest. 2018 Jan 2;128(1):233-247. doi: 10.1172/JCI95937. Epub 2017 Nov 27.

21.

At the dawn of personalized reproductive medicine: opportunities and challenges with incorporating multigene panel testing into fertility care.

Yurttas Beim P, Parfitt DE, Tan L, Sugarman EA, Hu-Seliger T, Clementi C, Levy B.

J Assist Reprod Genet. 2017 Dec;34(12):1573-1576. doi: 10.1007/s10815-017-1068-2. Epub 2017 Oct 23. No abstract available.

22.

Preface: Special Topic on Reaction Pathways.

Clementi C, Henkelman G.

J Chem Phys. 2017 Oct 21;147(15):152401. doi: 10.1063/1.5007080.

PMID:
29055311
23.

Combining experimental and simulation data of molecular processes via augmented Markov models.

Olsson S, Wu H, Paul F, Clementi C, Noé F.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8265-8270. doi: 10.1073/pnas.1704803114. Epub 2017 Jul 17.

24.
25.

An Abbreviated Version of the Mindful Eating Questionnaire.

Clementi C, Casu G, Gremigni P.

J Nutr Educ Behav. 2017 Apr;49(4):352-356.e1. doi: 10.1016/j.jneb.2017.01.016.

PMID:
28391799
26.

Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods.

Noé F, Clementi C.

Curr Opin Struct Biol. 2017 Apr;43:141-147. doi: 10.1016/j.sbi.2017.02.006. Epub 2017 Mar 17. Review.

PMID:
28327454
27.

BMP7 Induces Uterine Receptivity and Blastocyst Attachment.

Monsivais D, Clementi C, Peng J, Fullerton PT Jr, Prunskaite-Hyyryläinen R, Vainio SJ, Matzuk MM.

Endocrinology. 2017 Apr 1;158(4):979-992. doi: 10.1210/en.2016-1629.

28.

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling.

Noé F, Banisch R, Clementi C.

J Chem Theory Comput. 2016 Nov 8;12(11):5620-5630. Epub 2016 Oct 24.

PMID:
27696838
29.

[Quality end of life in uremic patients: theory and practice].

Galassi A, Giovenzana ME, Prolo F, Colombo AM, Orsi L, Fucci S, Sorbara L, Viganò S, Clementi C, Falcaro S, Auricchio S, Dozio B, Scanziani R.

G Ital Nefrol. 2016 May-Jun;33(3). pii: gin/33.3.4. Review. Italian.

PMID:
27374389
30.

SMAD Signaling Is Required for Structural Integrity of the Female Reproductive Tract and Uterine Function During Early Pregnancy in Mice.

Rodriguez A, Tripurani SK, Burton JC, Clementi C, Larina I, Pangas SA.

Biol Reprod. 2016 Aug;95(2):44. doi: 10.1095/biolreprod.116.139477. Epub 2016 Jun 22.

31.

Towards a semiquantitative non invasive characterisation of Tyrian purple dye composition: Convergence of UV-Visible reflectance spectroscopy and fast-high temperature-high performance liquid chromatography with photodiode array detection.

Clementi C, Nowik W, Romani A, Cardon D, Trojanowicz M, Davantès A, Chaminade P.

Anal Chim Acta. 2016 Jul 5;926:17-27. doi: 10.1016/j.aca.2016.04.022. Epub 2016 Apr 29.

PMID:
27216389
32.

The Role of pH in Modulating the Electronic State Properties of Minocycline Drug and Its Inclusion within Micellar Carriers.

Clementi C, Cesaretti A, Carlotti B, Elisei F.

J Phys Chem A. 2016 Jul 14;120(27):4994-5005. doi: 10.1021/acs.jpca.5b12707. Epub 2016 Mar 4.

PMID:
26909562
33.

Uterine ALK3 is essential during the window of implantation.

Monsivais D, Clementi C, Peng J, Titus MM, Barrish JP, Creighton CJ, Lydon JP, DeMayo FJ, Matzuk MM.

Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):E387-95. doi: 10.1073/pnas.1523758113. Epub 2015 Dec 31.

34.

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

Boninsegna L, Gobbo G, Noé F, Clementi C.

J Chem Theory Comput. 2015 Dec 8;11(12):5947-60. doi: 10.1021/acs.jctc.5b00749. Epub 2015 Nov 18.

PMID:
26580713
35.

Kinetic distance and kinetic maps from molecular dynamics simulation.

Noé F, Clementi C.

J Chem Theory Comput. 2015 Oct 13;11(10):5002-11. doi: 10.1021/acs.jctc.5b00553. Epub 2015 Sep 11.

PMID:
26574285
36.

Uterine Activin-Like Kinase 4 Regulates Trophoblast Development During Mouse Placentation.

Peng J, Fullerton PT Jr, Monsivais D, Clementi C, Su GH, Matzuk MM.

Mol Endocrinol. 2015 Dec;29(12):1684-93. doi: 10.1210/me.2015-1048. Epub 2015 Oct 20.

37.

Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype.

Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E402-9. doi: 10.1073/pnas.1416287112. Epub 2015 Jan 20.

38.

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C, Meuwly M.

J Chem Phys. 2015 Jan 14;142(2):025103. doi: 10.1063/1.4904431.

PMID:
25591387
39.

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

A Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003797. doi: 10.1371/journal.pcbi.1003797. eCollection 2014 Oct. Erratum in: PLoS Comput Biol. 2017 Sep 25;13(9):e1005770.

40.

Doxycycline and oxytetracycline loading of a zwitterionic amphoteric surfactant-gel and their controlled release.

Cesaretti A, Carlotti B, Gentili PL, Clementi C, Germani R, Elisei F.

Phys Chem Chem Phys. 2014 Nov 14;16(42):23096-107. doi: 10.1039/c4cp03488k.

PMID:
25251135
41.

Spectroscopic investigation of the pH controlled inclusion of doxycycline and oxytetracycline antibiotics in cationic micelles and their magnesium driven release.

Cesaretti A, Carlotti B, Gentili PL, Clementi C, Germani R, Elisei F.

J Phys Chem B. 2014 Jul 24;118(29):8601-13. doi: 10.1021/jp502278z. Epub 2014 Jul 10.

PMID:
24983832
42.

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

Preto J, Clementi C.

Phys Chem Chem Phys. 2014 Sep 28;16(36):19181-91. doi: 10.1039/c3cp54520b.

PMID:
24955434
43.

Effect of micellar and sol-gel media on the spectral and kinetic properties of tetracycline and its complexes with Mg²⁺.

Cesaretti A, Carlotti B, Clementi C, Germani R, Elisei F.

Photochem Photobiol Sci. 2014 Mar;13(3):509-20. doi: 10.1039/c3pp50314c. Epub 2013 Dec 18.

PMID:
24346739
44.

Activin-like kinase 2 functions in peri-implantation uterine signaling in mice and humans.

Clementi C, Tripurani SK, Large MJ, Edson MA, Creighton CJ, Hawkins SM, Kovanci E, Kaartinen V, Lydon JP, Pangas SA, DeMayo FJ, Matzuk MM.

PLoS Genet. 2013 Nov;9(11):e1003863. doi: 10.1371/journal.pgen.1003863. Epub 2013 Nov 14.

45.
46.

Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

Zheng W, Vargiu AV, Rohrdanz MA, Carloni P, Clementi C.

J Chem Phys. 2013 Oct 14;139(14):145102. doi: 10.1063/1.4824106. Erratum in: J Chem Phys. 2013 Dec 14;139(22):229901. Vargiu, Attlio Vittorio [corrected to Vargiu, Attilio Vittorio].

47.

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

Zheng W, Rohrdanz MA, Clementi C.

J Phys Chem B. 2013 Oct 24;117(42):12769-76. doi: 10.1021/jp401911h. Epub 2013 Aug 7.

48.

The Book of Kells: a non-invasive MOLAB investigation by complementary spectroscopic techniques.

Doherty B, Daveri A, Clementi C, Romani A, Bioletti S, Brunetti B, Sgamellotti A, Miliani C.

Spectrochim Acta A Mol Biomol Spectrosc. 2013 Nov;115:330-6. doi: 10.1016/j.saa.2013.06.020. Epub 2013 Jun 25.

PMID:
23850791
49.

[Psychological distress and personality characteristics among individuals with primary exercise dependence].

Guidi J, Clementi C, Grandi S.

Riv Psichiatr. 2013 Mar-Apr;48(2):121-9. doi: 10.1708/1272.14036. Italian.

PMID:
23748722
50.

BMPR2 is required for postimplantation uterine function and pregnancy maintenance.

Nagashima T, Li Q, Clementi C, Lydon JP, DeMayo FJ, Matzuk MM.

J Clin Invest. 2013 Jun;123(6):2539-50. doi: 10.1172/JCI65710. Epub 2013 May 8.

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