Martin Zacharias

Publication Activity (10 Years)

Years Active: 1990-2024
Publications (10 Years): 17

Top Topics

Protein Complexes

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Luis J. Walter, Patrick K. Quoika, Martin Zacharias
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations. J. Chem. Inf. Model. 64 (8) (2024)
Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias
for mono- and bimetallic ligand binding sites. J. Comput. Chem. 44 (8) (2023)
Richard L. Zschau, Martin Zacharias
-hairpin formation in AzoChignolin and Chignolin. J. Comput. Chem. 44 (9) (2023)
Mateusz Marcisz, Margrethe Gaardløs, Krzysztof K. Bojarski, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. J. Comput. Chem. 43 (24) (2022)
Maximilian Meixner, Martin Zachmann, Sebastian Metzler, Jonathan Scheerer, Martin Zacharias, Iris Antes
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock. J. Chem. Inf. Model. 62 (14) (2022)
Danial Pourjafar-Dehkordi, Martin Zacharias
Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling. PLoS Comput. Biol. 17 (11) (2021)
Martyna Maszota-Zieleniak, Mateusz Marcisz, Malgorzata M. Kogut, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. J. Comput. Chem. 42 (15) (2021)
Julian Hartmann, Martin Zacharias
Mechanism of collagen folding propagation studied by Molecular Dynamics simulations. PLoS Comput. Biol. 17 (6) (2021)
Mateusz Marcisz, Martin Zacharias, Sergey A. Samsonov
Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? J. Chem. Inf. Model. 61 (9) (2021)
Till Siebenmorgen, Michael Engelhard, Martin Zacharias
Prediction of protein-protein complexes using replica exchange with repulsive scaling. J. Comput. Chem. 41 (15) (2020)
Till Siebenmorgen, Martin Zacharias
Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling. J. Chem. Inf. Model. 60 (11) (2020)
Sergey A. Samsonov, Martin Zacharias, Isaure Chauvot de Beauchêne
Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. J. Comput. Chem. 40 (14) (2019)
Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci
Update of the ATTRACT force field for the prediction of protein-protein binding affinity. J. Comput. Chem. 38 (21) (2017)
Sjoerd J. de Vries, Martin Zacharias
Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. 38 (17) (2017)
Sjoerd J. de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry
The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Maria M. Reif, Martin Zacharias
Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J. Comput. Chem. 37 (18) (2016)
Isaure Chauvot de Beauchêne, Sjoerd J. de Vries, Martin Zacharias
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. PLoS Comput. Biol. 12 (1) (2016)
Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy, Pierre Tufféry
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Manuel P. Luitz, Martin Zacharias
Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials. J. Chem. Inf. Model. 54 (6) (2014)
Katja Ostermeir, Martin Zacharias
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. J. Comput. Chem. 35 (2) (2014)
Fabian Zeller, Martin Zacharias
Efficient calculation of relative binding free energies by umbrella sampling perturbation. J. Comput. Chem. 35 (31) (2014)
Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione
. PLoS Comput. Biol. 9 (6) (2013)
Piotr Setny, Ranjit Bahadur, Martin Zacharias
Protein-DNA docking with a coarse-grained force field. BMC Bioinform. 13 (2012)
Srinivasaraghavan Kannan, Wolfgang Sippl, Martin Zacharias
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent. J. Cheminformatics 3 (S-1) (2011)
Simon Leis, Martin Zacharias
Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J. Comput. Chem. 32 (16) (2011)
Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinform. 11 (2010)
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinform. 10 (2009)
Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping. J. Comput. Chem. 30 (3) (2009)
Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias
Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2. Silico Biol. 2 (3) (2002)
Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias
Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations. German Conference on Bioinformatics (2001)
Martin Zacharias, Heinz Sklenar
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J. Comput. Chem. 20 (3) (1999)
Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, James Andrew McCammon
A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. 16 (4) (1995)
Günter Theißen, Jürgen Eberle, Martin Zacharias, Luise Tobias, Rolf Wagner
The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions. Nucleic Acids Res. 18 (13) (1990)