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Items: 1 to 20 of 41

1.

Kinetics of Drug Binding and Residence Time.

Bernetti M, Masetti M, Rocchia W, Cavalli A.

Annu Rev Phys Chem. 2019 Jun 14;70:143-171. doi: 10.1146/annurev-physchem-042018-052340. Epub 2019 Feb 20.

PMID:
30786217
2.

Finding Principal Paths in Data Space.

Ferrarotti MJ, Rocchia W, Decherchi S.

IEEE Trans Neural Netw Learn Syst. 2019 Aug;30(8):2449-2462. doi: 10.1109/TNNLS.2018.2884792. Epub 2018 Dec 25.

PMID:
30596587
3.

NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.

Decherchi S, Spitaleri A, Stone J, Rocchia W.

Bioinformatics. 2019 Apr 1;35(7):1241-1243. doi: 10.1093/bioinformatics/bty761.

PMID:
30169777
4.

Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies.

Lapelosa M, Burrone O, Rocchia W.

ChemistryOpen. 2018 Aug 20;7(8):604-610. doi: 10.1002/open.201800121. eCollection 2018 Aug.

5.

Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.

Decherchi S, Bottegoni G, Spitaleri A, Rocchia W, Cavalli A.

J Chem Inf Model. 2018 Aug 27;58(8):1721. doi: 10.1021/acs.jcim.8b00489. Epub 2018 Aug 3. No abstract available.

6.

Including diverging electrostatic potential in 3D-RISM theory: The charged wall case.

Vyalov I, Rocchia W.

J Chem Phys. 2018 Mar 21;148(11):114106. doi: 10.1063/1.5019596.

PMID:
29566525
7.

Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach.

Spitaleri A, Decherchi S, Cavalli A, Rocchia W.

J Chem Theory Comput. 2018 Mar 13;14(3):1727-1736. doi: 10.1021/acs.jctc.7b01088. Epub 2018 Feb 9.

PMID:
29351374
8.

BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.

Decherchi S, Bottegoni G, Spitaleri A, Rocchia W, Cavalli A.

J Chem Inf Model. 2018 Feb 26;58(2):219-224. doi: 10.1021/acs.jcim.7b00680. Epub 2018 Jan 31. Erratum in: J Chem Inf Model. 2018 Aug 27;58(8):1721.

PMID:
29338240
9.

Force Field Parametrization of Metal Ions from Statistical Learning Techniques.

Fracchia F, Del Frate G, Mancini G, Rocchia W, Barone V.

J Chem Theory Comput. 2018 Jan 9;14(1):255-273. doi: 10.1021/acs.jctc.7b00779. Epub 2017 Dec 6.

10.

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis.

La Sala G, Decherchi S, De Vivo M, Rocchia W.

ACS Cent Sci. 2017 Sep 27;3(9):949-960. doi: 10.1021/acscentsci.7b00211. Epub 2017 Aug 10.

11.

Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor.

Zia SR, Gaspari R, Decherchi S, Rocchia W.

J Chem Theory Comput. 2016 Dec 13;12(12):6049-6061. Epub 2016 Nov 10.

PMID:
27951680
12.

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.

Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A.

Front Mol Biosci. 2016 Aug 31;3:46. doi: 10.3389/fmolb.2016.00046. eCollection 2016.

13.
14.

Corrigendum: Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.

Mollica L, Decherchi S, Zia SR, Gaspari R, Cavalli A, Rocchia W.

Sci Rep. 2016 May 6;6:25299. doi: 10.1038/srep25299. No abstract available.

15.

Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm.

Decherchi S, Rocchia W.

IEEE Trans Neural Netw Learn Syst. 2017 Jul;28(7):1722-1729. doi: 10.1109/TNNLS.2016.2547220. Epub 2016 Apr 12.

PMID:
27093710
16.

A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using quantitative nuclear magnetic resonance.

Goldoni L, Beringhelli T, Rocchia W, Realini N, Piomelli D.

Anal Biochem. 2016 May 15;501:26-34. doi: 10.1016/j.ab.2016.02.009. Epub 2016 Feb 18.

PMID:
26898303
17.

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.

Gaspari R, Rechlin C, Heine A, Bottegoni G, Rocchia W, Schwarz D, Bomke J, Gerber HD, Klebe G, Cavalli A.

J Med Chem. 2016 May 12;59(9):4245-56. doi: 10.1021/acs.jmedchem.5b01643. Epub 2016 Jan 12.

PMID:
26700575
18.

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

Spyrakis F, Benedetti P, Decherchi S, Rocchia W, Cavalli A, Alcaro S, Ortuso F, Baroni M, Cruciani G.

J Chem Inf Model. 2015 Oct 26;55(10):2256-74. doi: 10.1021/acs.jcim.5b00169. Epub 2015 Sep 22.

19.

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.

Mollica L, Decherchi S, Zia SR, Gaspari R, Cavalli A, Rocchia W.

Sci Rep. 2015 Jun 23;5:11539. doi: 10.1038/srep11539. Erratum in: Sci Rep. 2016 May 06;6:25299.

20.

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

Decherchi S, Berteotti A, Bottegoni G, Rocchia W, Cavalli A.

Nat Commun. 2015 Jan 27;6:6155. doi: 10.1038/ncomms7155.

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