Matteo T Degiacomi

Matteo T Degiacomi

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Matteo T Degiacomi

Matteo T Degiacomi

Publications by authors named "Matteo T Degiacomi"

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Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics.

J Chem Theory Comput 2019 Sep 21;15(9):5135-5143. Epub 2019 Aug 21.

Department of Chemistry , Durham University , South Road , Durham DH1 3LE , U.K.

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http://dx.doi.org/10.1021/acs.jctc.9b00474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007192PMC
September 2019

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.

Structure 2019 06 25;27(6):1034-1040.e3. Epub 2019 Apr 25.

Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.03.018DOI Listing
June 2019

Structural and functional consequences of age-related isomerization in α-crystallins.

J Biol Chem 2019 05 25;294(19):7546-7555. Epub 2019 Feb 25.

From the Department of Chemistry, University of California, Riverside, Riverside, California 92521,

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http://dx.doi.org/10.1074/jbc.RA118.007052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6514633PMC
May 2019

On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies.

J Am Soc Mass Spectrom 2019 Jan 7;30(1):113-117. Epub 2018 May 7.

Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.

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http://link.springer.com/10.1007/s13361-018-1974-2
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http://dx.doi.org/10.1007/s13361-018-1974-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318233PMC
January 2019

It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate.

J Biol Chem 2018 12 22;293(51):19511-19521. Epub 2018 Oct 22.

From the Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003,

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA118.005421
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http://dx.doi.org/10.1074/jbc.RA118.005421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314120PMC
December 2018

Mineral surface chemistry control for origin of prebiotic peptides.

Nat Commun 2017 12 11;8(1):2033. Epub 2017 Dec 11.

Department of Earth Sciences, Durham University, South Road, Durham, DH1 3LE, UK.

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http://www.nature.com/articles/s41467-017-02248-y
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http://dx.doi.org/10.1038/s41467-017-02248-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725419PMC
December 2017

Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks.

Structure 2017 11 28;25(11):1751-1757.e5. Epub 2017 Sep 28.

Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.08.015DOI Listing
November 2017

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

J Am Chem Soc 2017 07 10;139(28):9523-9533. Epub 2017 Jul 10.

Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, Oxfordshire OX1 3QZ, U.K.

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http://dx.doi.org/10.1021/jacs.6b11358DOI Listing
July 2017

The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans.

Structure 2017 05 20;25(5):773-782.e5. Epub 2017 Apr 20.

Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK; Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.03.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5556678PMC
May 2017

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies.

Sci Rep 2017 03 22;7(1):235. Epub 2017 Mar 22.

Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.

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http://dx.doi.org/10.1038/s41598-017-00266-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427971PMC
March 2017

Integrating mass spectrometry with MD simulations reveals the role of lipids in Na/H antiporters.

Nat Commun 2017 01 10;8:13993. Epub 2017 Jan 10.

Department of Chemistry, Physical &Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK.

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http://dx.doi.org/10.1038/ncomms13993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234078PMC
January 2017

EM∩IM: software for relating ion mobility mass spectrometry and electron microscopy data.

Analyst 2016 Jan 30;141(1):70-5. Epub 2015 Nov 30.

Department of Chemistry, Physical & Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.

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http://dx.doi.org/10.1039/c5an01636cDOI Listing
January 2016

A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis.

EMBO Mol Med 2015 Oct;7(10):1337-49

Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London, UK Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Pavia, Italy

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http://dx.doi.org/10.15252/emmm.201505357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604687PMC
October 2015

Collision cross sections for structural proteomics.

Structure 2015 Apr 19;23(4):791-9. Epub 2015 Mar 19.

Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.str.2015.02.010DOI Listing
April 2015

A subset of annular lipids is linked to the flippase activity of an ABC transporter.

Nat Chem 2015 Mar 2;7(3):255-62. Epub 2015 Feb 2.

Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.

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http://dx.doi.org/10.1038/nchem.2172DOI Listing
March 2015

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.

Nat Chem Biol 2013 Oct 4;9(10):623-9. Epub 2013 Aug 4.

1] Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [2] [3].

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http://dx.doi.org/10.1038/nchembio.1312DOI Listing
October 2013

Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins.

J Chem Theory Comput 2013 Aug 11;9(8):3515-26. Epub 2013 Jul 11.

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne-EPFL , Lausanne, CH-1015, Switzerland.

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http://dx.doi.org/10.1021/ct400137qDOI Listing
August 2013

Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling.

Structure 2013 Jul;21(7):1097-1106

Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fe´ de´ rale de Lausanne - EPFL, CH-1025 Lausanne.

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http://dx.doi.org/10.1016/j.str.2013.05.014DOI Listing
July 2013

Arranged sevenfold: structural insights into the C-terminal oligomerization domain of human C4b-binding protein.

J Mol Biol 2013 Apr 28;425(8):1302-17. Epub 2012 Dec 28.

Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstraße 22, 64287 Darmstadt, Germany.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836120095
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http://dx.doi.org/10.1016/j.jmb.2012.12.017DOI Listing
April 2013