Cavalli A - Search Results

1

Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5.

Patel JS, Berteotti A, Ronsisvalle S, Rocchia W, Cavalli A. Patel JS, et al. Among authors: cavalli a. J Chem Inf Model. 2014 Feb 24;54(2):470-80. doi: 10.1021/ci4003574. Epub 2014 Jan 28. J Chem Inf Model. 2014. PMID: 24437446

2

A comparative study on the application of hierarchical-agglomerative clustering approaches to organize outputs of reiterated docking runs.

Bottegoni G, Cavalli A, Recanatini M. Bottegoni G, et al. Among authors: cavalli a. J Chem Inf Model. 2006 Mar-Apr;46(2):852-62. doi: 10.1021/ci050141q. J Chem Inf Model. 2006. PMID: 16563017

3

AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets.

Bottegoni G, Rocchia W, Recanatini M, Cavalli A. Bottegoni G, et al. Among authors: cavalli a. Bioinformatics. 2006 Jul 15;22(14):e58-65. doi: 10.1093/bioinformatics/btl212. Bioinformatics. 2006. PMID: 16873522

4

Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations.

Berteotti A, Cavalli A, Branduardi D, Gervasio FL, Recanatini M, Parrinello M. Berteotti A, et al. Among authors: cavalli a. J Am Chem Soc. 2009 Jan 14;131(1):244-50. doi: 10.1021/ja806846q. J Am Chem Soc. 2009. PMID: 19067513

5

Systematic exploitation of multiple receptor conformations for virtual ligand screening.

Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A. Bottegoni G, et al. Among authors: cavalli a. PLoS One. 2011;6(5):e18845. doi: 10.1371/journal.pone.0018845. Epub 2011 May 17. PLoS One. 2011. PMID: 21625529 Free PMC article.

6

Cyclin-dependent kinases: bridging their structure and function through computations.

De Vivo M, Bottegoni G, Berteotti A, Recanatini M, Gervasio FL, Cavalli A. De Vivo M, et al. Among authors: cavalli a. Future Med Chem. 2011 Sep;3(12):1551-9. doi: 10.4155/fmc.11.113. Future Med Chem. 2011. PMID: 21882947 Review.

7

SERAPhiC: a benchmark for in silico fragment-based drug design.

Favia AD, Bottegoni G, Nobeli I, Bisignano P, Cavalli A. Favia AD, et al. Among authors: cavalli a. J Chem Inf Model. 2011 Nov 28;51(11):2882-96. doi: 10.1021/ci2003363. Epub 2011 Oct 12. J Chem Inf Model. 2011. PMID: 21936510

8

Insights into Ligand-Protein Binding from Local Mechanical Response.

Patel JS, Branduardi D, Masetti M, Rocchia W, Cavalli A. Patel JS, et al. Among authors: cavalli a. J Chem Theory Comput. 2011 Oct 11;7(10):3368-3378. doi: 10.1021/ct200324j. Epub 2011 Aug 30. J Chem Theory Comput. 2011. PMID: 22003321 Free PMC article.

9

Application of conformational clustering in protein-ligand docking.

Bottegoni G, Rocchia W, Cavalli A. Bottegoni G, et al. Among authors: cavalli a. Methods Mol Biol. 2012;819:169-86. doi: 10.1007/978-1-61779-465-0_12. Methods Mol Biol. 2012. PMID: 22183537

10

In silico deconstruction of ATP-competitive inhibitors of glycogen synthase kinase-3β.

Bisignano P, Lambruschini C, Bicego M, Murino V, Favia AD, Cavalli A. Bisignano P, et al. Among authors: cavalli a. J Chem Inf Model. 2012 Dec 21;52(12):3233-44. doi: 10.1021/ci300355p. Epub 2012 Dec 12. J Chem Inf Model. 2012. PMID: 23198830

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