Martin Zacharias

Martin Zacharias

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Martin Zacharias

Martin Zacharias

Publications by authors named "Martin Zacharias"

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Molecular mechanism of Be-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding.

Phys Chem Chem Phys 2020 Jan;22(2):799-810

Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi 682 022, India.

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http://dx.doi.org/10.1039/c9cp05695eDOI Listing
January 2020

The structure and oxidation of the eye lens chaperone αA-crystallin.

Nat Struct Mol Biol 2019 Dec 2;26(12):1141-1150. Epub 2019 Dec 2.

Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1038/s41594-019-0332-9DOI Listing
December 2019

Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach.

Proteins 2019 Nov 30. Epub 2019 Nov 30.

Physik-Department T38, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1002/prot.25860DOI Listing
November 2019

The Architecture of Talin1 Reveals an Autoinhibition Mechanism.

Cell 2019 Sep;179(1):120-131.e13

Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856716PMC
September 2019

Global Dynamics of Yeast Hsp90 Middle and C-Terminal Dimer Studied by Advanced Sampling Simulations.

Front Mol Biosci 2019 27;6:93. Epub 2019 Sep 27.

Physics Department T38, Technical University of Munich, Garching, Germany.

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http://dx.doi.org/10.3389/fmolb.2019.00093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798034PMC
September 2019

Prognostic value of cyclin A2 and B1 expression in lung carcinoids.

Pathology 2019 Aug 20;51(5):481-486. Epub 2019 Jun 20.

Medical University of Graz, Diagnostic and Research Institute of Pathology, Graz, Austria.

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http://dx.doi.org/10.1016/j.pathol.2019.03.011DOI Listing
August 2019

Uncovering the Binding Mode of γ -Secretase Inhibitors.

ACS Chem Neurosci 2019 Aug 25;10(8):3398-3403. Epub 2019 Jun 25.

Physics Department T38 , Technical University of Munich , James-Frank-Strasse 1 , 85748 Garching , Germany.

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http://dx.doi.org/10.1021/acschemneuro.9b00272DOI Listing
August 2019

Phosphorylation of Ser111 in Rab8a Modulates Rabin8-Dependent Activation by Perturbation of Side Chain Interaction Networks.

Biochemistry 2019 Aug 8;58(33):3546-3554. Epub 2019 Aug 8.

Physics Department T38 , Technical University of Munich , James-Franck-Strasse 1 , 85748 Garching , Germany.

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http://dx.doi.org/10.1021/acs.biochem.9b00516DOI Listing
August 2019

Modeling large protein-glycosaminoglycan complexes using a fragment-based approach.

J Comput Chem 2019 May 15;40(14):1429-1439. Epub 2019 Feb 15.

CNRS, LORIA (CNRS, Inria NGE, Université de Lorraine), Campus Scientifique, 615 rue du Jardin Botanique, Vandœuvre-lès-Nancy, F-54506, France.

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http://doi.wiley.com/10.1002/jcc.25797
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http://dx.doi.org/10.1002/jcc.25797DOI Listing
May 2019

An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27.

J Mol Biol 2019 May 26;431(12):2383-2393. Epub 2019 Apr 26.

Center for Integrated Protein Science at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.04.032DOI Listing
May 2019

Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations.

Authors:
Martin Zacharias

Angew Chem Int Ed Engl 2019 Apr 26;58(18):5967-5972. Epub 2019 Mar 26.

Physics Department T38, Technical University of Munich, 85748, Garching, Germany.

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http://dx.doi.org/10.1002/anie.201900935DOI Listing
April 2019

Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations.

J Chem Theory Comput 2019 Mar 15;15(3):2071-2086. Epub 2019 Feb 15.

Physik-Department T38 , Technische Universität München , James-Franck-Strasse 1 , 85748 Garching , Germany.

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http://dx.doi.org/10.1021/acs.jctc.8b01022DOI Listing
March 2019

How methyl-sugar interactions determine DNA structure and flexibility.

Nucleic Acids Res 2019 02;47(3):1132-1140

Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379717PMC
February 2019

The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding.

J Mol Biol 2019 Jan 17;431(2):223-243. Epub 2018 Oct 17.

Physics Department (T38), Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836183069
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http://dx.doi.org/10.1016/j.jmb.2018.09.015DOI Listing
January 2019

A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine.

Proc Natl Acad Sci U S A 2019 01 16;116(5):1585-1590. Epub 2019 Jan 16.

Center for Integrated Protein Science, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1816698116
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http://dx.doi.org/10.1073/pnas.1816698116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358668PMC
January 2019

A single residue switch reveals principles of antibody domain integrity.

J Biol Chem 2018 11 18;293(44):17107-17118. Epub 2018 Sep 18.

From the Center for Integrated Protein Science Munich, Departments of Chemie and

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http://dx.doi.org/10.1074/jbc.RA118.005475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222096PMC
November 2018

The temperature dependence of the helical twist of DNA.

Nucleic Acids Res 2018 09;46(15):7998-8009

Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.

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http://dx.doi.org/10.1093/nar/gky599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125625PMC
September 2018

Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.

Proc Natl Acad Sci U S A 2018 08 23;115(32):E7512-E7521. Epub 2018 Jul 23.

Laboratory for Biomolecular Design, Physics Department, Technische Universität München, 85748 Garching, Germany;

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http://dx.doi.org/10.1073/pnas.1800585115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6094131PMC
August 2018

Bulk tumour cell migration in lung carcinomas might be more common than epithelial-mesenchymal transition and be differently regulated.

BMC Cancer 2018 Jul 6;18(1):717. Epub 2018 Jul 6.

Diagnostic and Research Center, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstraße 6, Graz, 8036, Austria.

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http://dx.doi.org/10.1186/s12885-018-4640-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034257PMC
July 2018

Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions.

Methods Mol Biol 2017 ;1561:49-68

Physics Department (T38), Center for Integrated Protein Science Munich (CIPSM), Technical University of Munich, James-Franck-Str. 1, 85748, Garching, Germany.

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http://link.springer.com/10.1007/978-1-4939-6798-8_5
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http://dx.doi.org/10.1007/978-1-4939-6798-8_5DOI Listing
February 2018

Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling.

Structure 2018 02 27;26(2):282-294.e6. Epub 2018 Jan 27.

Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.12.015DOI Listing
February 2018

Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations.

J Phys Chem B 2017 12 19;121(49):11019-11030. Epub 2017 Nov 19.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1021/acs.jpcb.7b07701DOI Listing
December 2017

Multiscale Simulation of Receptor-Drug Association Kinetics: Application to Neuraminidase Inhibitors.

J Chem Theory Comput 2017 Oct 6;13(10):5097-5105. Epub 2017 Sep 6.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1021/acs.jctc.7b00631DOI Listing
October 2017

Comparative Molecular Dynamics Analysis of RNase-S Complex Formation.

Biophys J 2017 Oct;113(7):1466-1474

Physik Department, T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science, Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627186PMC
October 2017

Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction amyloid self-assembly.

J Biol Chem 2017 09 6;292(35):14587-14602. Epub 2017 Jul 6.

From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and

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http://dx.doi.org/10.1074/jbc.M117.774893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582850PMC
September 2017

Determinants of the assembly and function of antibody variable domains.

Sci Rep 2017 09 25;7(1):12276. Epub 2017 Sep 25.

Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.

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http://dx.doi.org/10.1038/s41598-017-12519-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613017PMC
September 2017

Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential.

PLoS One 2017 16;12(2):e0172072. Epub 2017 Feb 16.

Physik-Department T38, Technische Universität München, Garching, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172072PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313199PMC
August 2017

The pepATTRACT web server for blind, large-scale peptide-protein docking.

Nucleic Acids Res 2017 07;45(W1):W361-W364

INSERM UMR-S 973/Université Paris Diderot/Sorbonne Paris Cité/RPBS, Paris 75205, France.

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http://dx.doi.org/10.1093/nar/gkx335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570166PMC
July 2017

Fast and accurate grid representations for atom-based docking with partner flexibility.

J Comput Chem 2017 06 2;38(17):1538-1546. Epub 2017 May 2.

MTi, UMR-S 973, Physics Department T38, Technische Universität München, James-Franck-Strasse 1, 85748, Garching, Germany.

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http://doi.wiley.com/10.1002/jcc.24795
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http://dx.doi.org/10.1002/jcc.24795DOI Listing
June 2017

Thermodynamics and Kinetics of Nucleobase Stacking Oligomerization Revealed by Molecular Dynamics Simulations.

J Chem Theory Comput 2017 Jun 19;13(6):3005-3011. Epub 2017 May 19.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany.

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http://pubs.acs.org/doi/10.1021/acs.jctc.7b00150
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http://dx.doi.org/10.1021/acs.jctc.7b00150DOI Listing
June 2017

Update of the ATTRACT force field for the prediction of protein-protein binding affinity.

J Comput Chem 2017 06 5;38(21):1887-1890. Epub 2017 Jun 5.

Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, 06108 Nice, France.

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http://dx.doi.org/10.1002/jcc.24836DOI Listing
June 2017

Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations.

Biophys J 2017 Jun;112(11):2280-2290

Physics Department, Technical University of Munich, Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.04.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474742PMC
June 2017

Optical control of a receptor-linked guanylyl cyclase using a photoswitchable peptidic hormone.

Chem Sci 2017 Jun 19;8(6):4644-4653. Epub 2017 Apr 19.

Department of Chemistry and Center for Integrated Protein Science , LMU Munich , Butenandtstr. 5-13 , 81377 Munich , Germany . Email: ; Email:

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http://dx.doi.org/10.1039/c6sc05044aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471452PMC
June 2017

Monte Carlo replica-exchange based ensemble docking of protein conformations.

Proteins 2017 05 16;85(5):924-937. Epub 2017 Feb 16.

Physik-Department T38, Technische Universität München, Garching, 85748, Germany.

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http://doi.wiley.com/10.1002/prot.25262
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http://dx.doi.org/10.1002/prot.25262DOI Listing
May 2017

Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation.

J Phys Chem B 2017 04 4;121(15):3387-3393. Epub 2016 Nov 4.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1021/acs.jpcb.6b08597DOI Listing
April 2017

Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI.

Proteins 2017 03 24;85(3):391-398. Epub 2016 Nov 24.

Physics Department T38, Technische Universität München, Garching, 85748, Germany.

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http://dx.doi.org/10.1002/prot.25196DOI Listing
March 2017

Predicting Allosteric Changes from Conformational Ensembles.

Authors:
Martin Zacharias

Structure 2017 03;25(3):393-394

Physics Department T38, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany; Center for Integrated Protein Science, 81377 Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.02.006DOI Listing
March 2017

Multidomain structure and correlated dynamics determined by self-consistent FRET networks.

Nat Methods 2017 02 5;14(2):174-180. Epub 2016 Dec 5.

Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.

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http://dx.doi.org/10.1038/nmeth.4081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289555PMC
February 2017

From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

J Phys Chem B 2017 02 18;121(4):671-682. Epub 2017 Jan 18.

Physik Department, Technische Universität München , 85748 Garching, Germany.

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http://dx.doi.org/10.1021/acs.jpcb.6b10189DOI Listing
February 2017

Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage.

Sci Rep 2017 01 27;7:41324. Epub 2017 Jan 27.

Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany.

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http://dx.doi.org/10.1038/srep41324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269681PMC
January 2017

Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA.

Nucleic Acids Res 2016 Nov 19;44(20):9591-9599. Epub 2016 Sep 19.

Physik-Department T38, Technische Universität München, James-Franck-Straße 1, D-85748 Garching, Germany

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http://dx.doi.org/10.1093/nar/gkw827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175360PMC
November 2016

Free energy analysis and mechanism of base pair stacking in nicked DNA.

Nucleic Acids Res 2016 09 12;44(15):7100-8. Epub 2016 Jul 12.

Physik-Department T38, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany

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http://dx.doi.org/10.1093/nar/gkw607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009751PMC
September 2016

Single-molecule dissection of stacking forces in DNA.

Science 2016 09;353(6304)

Labor für Biomolekulare Nanotechnologie, Physik Department and Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, Germany. Munich Center for Integrated Protein Science, 81377 Munich, Germany. Institute for Advanced Study, TUM, Germany.

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http://dx.doi.org/10.1126/science.aaf5508DOI Listing
September 2016

Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations.

J Phys Chem B 2016 08 20;120(33):8186-92. Epub 2016 Apr 20.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1021/acs.jpcb.6b01792DOI Listing
August 2016

SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes.

Structure 2016 08 14;24(8):1387-1397. Epub 2016 Jul 14.

Physics Department (T38), Technische Universität München, 85748 Garching, Germany; Center for Integrated Protein Science, 81377 Munich, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.str.2016.06.007DOI Listing
August 2016

Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules.

J Comput Chem 2016 07 17;37(18):1711-24. Epub 2016 May 17.

Physics Department (T38), Technische Universität München, James-Franck-Str. 1, 85748, Garching, Germany.

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http://dx.doi.org/10.1002/jcc.24390DOI Listing
July 2016

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins.

Nucleic Acids Res 2016 06 29;44(10):4565-80. Epub 2016 Apr 29.

Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany

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http://dx.doi.org/10.1093/nar/gkw328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889956PMC
June 2016

Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins.

J Mol Biol 2016 Apr 4;428(8):1544-57. Epub 2016 Mar 4.

Center for Integrated Protein Science, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.02.028DOI Listing
April 2016

A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions.

J Mol Biol 2016 Mar 29;428(6):1315-1332. Epub 2016 Jan 29.

Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.01.015DOI Listing
March 2016

An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA.

PLoS One 2015 18;10(3):e0116414. Epub 2015 Mar 18.

Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116414PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364692PMC
February 2016

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

PLoS One 2015 8;10(6):e0125941. Epub 2015 Jun 8.

Physik-Department T38, Technische Universität München, James-Franck-Str. 1, 84748 Garching, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125941PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4459952PMC
February 2016

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.

Biophys J 2016 Feb 1;110(4):785-97. Epub 2016 Feb 1.

Physik-Department T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1016/j.bpj.2015.12.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776041PMC
February 2016

Subnanometre enzyme mechanics probed by single-molecule force spectroscopy.

Nat Commun 2016 Feb 24;7:10848. Epub 2016 Feb 24.

Physik Department E22, Technische Universität München, James Franck Strasse 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1038/ncomms10848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770092PMC
February 2016

Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step.

J Am Chem Soc 2016 Jan 6;138(2):527-39. Epub 2016 Jan 6.

Physik Department, Technische Universität München , 85748 Garching, Germany.

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http://dx.doi.org/10.1021/jacs.5b08717DOI Listing
January 2016

Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study.

Langmuir 2016 Jan 12;32(3):810-21. Epub 2016 Jan 12.

Institute of Physical Chemistry, University of Freiburg , 79104 Freiburg, Germany.

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http://dx.doi.org/10.1021/acs.langmuir.5b03435DOI Listing
January 2016

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.

PLoS Comput Biol 2016 Jan 27;12(1):e1004697. Epub 2016 Jan 27.

Physik-Department T38, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1004697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729675PMC
January 2016

Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis.

Sci Rep 2016 Jan 28;6:19896. Epub 2016 Jan 28.

Physics Department T38, Technische Universität München, 85748 Garching, Germany.

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http://dx.doi.org/10.1038/srep19896DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730224PMC
January 2016

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Nucleic Acids Res 2015 Dec 12;43(21):10143-56. Epub 2015 Oct 12.

Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany

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http://dx.doi.org/10.1093/nar/gkv1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666353PMC
December 2015

The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation.

J Mol Biol 2015 Nov 25;427(22):3572-3586. Epub 2015 Sep 25.

Center for Integrated Protein Science at the Department Chemie, Technische Universität München Lichtenbergstrasse 4, D-85747 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.09.012DOI Listing
November 2015

Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.

Biophys J 2015 Nov;109(9):1978-85

Physics Department, Technical University Munich, Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.08.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643206PMC
November 2015

Fully Blind Peptide-Protein Docking with pepATTRACT.

Structure 2015 Aug 2;23(8):1507-1515. Epub 2015 Jul 2.

Physics Department T38, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09692126150022
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http://dx.doi.org/10.1016/j.str.2015.05.021DOI Listing
August 2015

Exploring biomolecular dynamics and interactions using advanced sampling methods.

J Phys Condens Matter 2015 Aug 21;27(32):323101. Epub 2015 Jul 21.

Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1088/0953-8984/27/32/323101DOI Listing
August 2015

Influence of a cis,syn-cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations.

Biopolymers 2015 Apr;103(4):215-22

Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany.

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http://dx.doi.org/10.1002/bip.22586DOI Listing
April 2015

Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces.

Methods Mol Biol 2014 ;1184:365-74

Faculté des Sciences, UMR-CNRS 7272, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Nice Cedex 2, 06108, France,

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http://dx.doi.org/10.1007/978-1-4939-1115-8_20DOI Listing
March 2015

Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations.

Mol Immunol 2015 Feb 18;63(2):312-9. Epub 2014 Aug 18.

Physik-Department T38, Technische Universität München, James Franck Street 1, 85748 Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molimm.2014.07.021DOI Listing
February 2015

iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement.

Proteins 2015 Feb 18;83(2):248-58. Epub 2014 Dec 18.

Physik Department T38, Technische Universität München, 85748, Garching, Germany.

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http://dx.doi.org/10.1002/prot.24728DOI Listing
February 2015

A web interface for easy flexible protein-protein docking with ATTRACT.

Biophys J 2015 Feb;108(3):462-5

Physics Department, Technische Universität München, Garching, Germany.

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http://dx.doi.org/10.1016/j.bpj.2014.12.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317529PMC
February 2015

A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain.

Biophys J 2015 Feb;108(3):678-86

Physik Department E22, Technische Universität München, Garching, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2014.11.3482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317555PMC
February 2015

Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations.

Biopolymers 2015 Jan;103(1):23-32

Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748, Garching, Germany.

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http://dx.doi.org/10.1002/bip.22535DOI Listing
January 2015

Rapid alchemical free energy calculation employing a generalized born implicit solvent model.

J Phys Chem B 2015 Jan 11;119(3):968-75. Epub 2014 Sep 11.

Physik-Department T38, Technische Universität München , Garching, Germany.

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http://dx.doi.org/10.1021/jp506367yDOI Listing
January 2015

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

Proteins 2014 Dec 10;82(12):3410-9. Epub 2014 Oct 10.

Physik-Department T38, Technische Universität München, 85748, Garching, Germany.

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http://dx.doi.org/10.1002/prot.24695DOI Listing
December 2014

Efficient calculation of relative binding free energies by umbrella sampling perturbation.

J Comput Chem 2014 Dec 30;35(31):2256-62. Epub 2014 Sep 30.

Physik-Department T38, Technische Universität München, Garching, Germany.

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http://doi.wiley.com/10.1002/jcc.23744
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December 2014

A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

J Biol Chem 2014 Sep 5;289(39):26829-46. Epub 2014 Aug 5.

From the Center for Integrated Protein Science, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany,

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http://dx.doi.org/10.1074/jbc.M114.582247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175325PMC
September 2014

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.

Nucleic Acids Res 2014 Jul 6;42(Web Server issue):W221-6. Epub 2014 May 6.

INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France

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http://nar.oxfordjournals.org/content/early/2014/05/06/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku404
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http://dx.doi.org/10.1093/nar/gku404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086095PMC
July 2014

Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations.

J Phys Chem B 2014 Jul 27;118(27):7467-7474. Epub 2014 Jun 27.

Physik-Department T38, Technische Universität München , James-Franck-Str. 1, Garching 85748, Germany.

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http://dx.doi.org/10.1021/jp5015934DOI Listing
July 2014

Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials.

J Chem Inf Model 2014 Jun 9;54(6):1669-75. Epub 2014 Jun 9.

Physik-Department T38, Technische Universität München , James Franck Str. 1, 85748 Garching, Germany.

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http://dx.doi.org/10.1021/ci500296fDOI Listing
June 2014

Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations.

J Chem Theory Comput 2014 Feb;10(2):703-10

Physik-Department T38, Technische Universität München , James Franck Str. 1, 85748 Garching, Germany.

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http://pubs.acs.org/doi/10.1021/ct400689h
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http://dx.doi.org/10.1021/ct400689hDOI Listing
February 2014

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

Glycobiology 2014 Jan 16;24(1):70-84. Epub 2013 Oct 16.

Central European Institute of Technology, Masaryk University, Kamenice 5, 61137 Brno, Czech Republic.

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http://dx.doi.org/10.1093/glycob/cwt093DOI Listing
January 2014

A novel family of human leukocyte antigen class II receptors may have its origin in archaic human species.

J Biol Chem 2014 Jan 8;289(2):639-53. Epub 2013 Nov 8.

From the Section of Immunobiology, Institute of Genetics, University of Bonn, 53115 Bonn, Germany.

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http://dx.doi.org/10.1074/jbc.M113.515767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887193PMC
January 2014

Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

J Comput Chem 2014 Jan 31;35(2):150-8. Epub 2013 Oct 31.

Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.

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http://dx.doi.org/10.1002/jcc.23476DOI Listing
January 2014

Flexible docking and refinement with a coarse-grained protein model using ATTRACT.

Proteins 2013 Dec 17;81(12):2167-74. Epub 2013 Oct 17.

Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.

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http://doi.wiley.com/10.1002/prot.24400
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December 2013

Elastic Network Models of Nucleic Acids Flexibility.

J Chem Theory Comput 2013 Dec 22;9(12):5460-70. Epub 2013 Nov 22.

Physics Department T38, Technical University Munich , 85748 Garching, Germany.

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http://dx.doi.org/10.1021/ct400814nDOI Listing
December 2013

Effect of 8-oxoguanine on DNA structure and deformability.

J Phys Chem B 2013 Oct 20;117(39):11617-22. Epub 2013 Sep 20.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstı́ 2, 166 10, Praha 6, Czech Republic.

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http://dx.doi.org/10.1021/jp407562tDOI Listing
October 2013

Dipeptides promote folding and peptide binding of MHC class I molecules.

Proc Natl Acad Sci U S A 2013 Sep 3;110(38):15383-8. Epub 2013 Sep 3.

Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1308672110
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http://dx.doi.org/10.1073/pnas.1308672110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3780906PMC
September 2013