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Journal Articles
- 2024
[j32]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): 3465-3476 (2024)- 2023
- [j31]Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias:
Benchmarking biomolecular force field-based Zn2+ for mono- and bimetallic ligand binding sites. J. Comput. Chem. 44(8): 912-926 (2023) - [j30]Richard L. Zschau, Martin Zacharias:
Mechanism of β-hairpin formation in AzoChignolin and Chignolin. J. Comput. Chem. 44(9): 988-1001 (2023) - 2022
- [j29]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): 1633-1640 (2022) - [j28]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): 3426-3441 (2022) - 2021
- [j27]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): 1040-1053 (2021) - [j26]Mateusz Marcisz, Martin Zacharias, Sergey A. Samsonov:
Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? J. Chem. Inf. Model. 61(9): 4475-4485 (2021) - [j25]Julian Hartmann, Martin Zacharias:
Mechanism of collagen folding propagation studied by Molecular Dynamics simulations. PLoS Comput. Biol. 17(6) (2021) - [j24]Danial Pourjafar-Dehkordi, Martin Zacharias:
Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling. PLoS Comput. Biol. 17(11) (2021) - 2020
- [j23]Till Siebenmorgen, Michael Engelhard, Martin Zacharias:
Prediction of protein-protein complexes using replica exchange with repulsive scaling. J. Comput. Chem. 41(15): 1436-1447 (2020) - [j22]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): 5552-5562 (2020) - 2019
- [j21]Sergey A. Samsonov, Martin Zacharias, Isaure Chauvot de Beauchêne:
Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. J. Comput. Chem. 40(14): 1429-1439 (2019) - 2017
- [j20]Sjoerd Jacob de Vries, Martin Zacharias:
Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. 38(17): 1538-1546 (2017) - [j19]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): 1887-1890 (2017) - [j18]Sjoerd Jacob 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): W361-W364 (2017) - 2016
- [j17]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): 1711-1724 (2016) - [j16]Isaure Chauvot de Beauchêne, Sjoerd Jacob 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) - 2014
- [j15]Katja Ostermeir, Martin Zacharias:
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. J. Comput. Chem. 35(2): 150-158 (2014) - [j14]Fabian Zeller, Martin Zacharias:
Efficient calculation of relative binding free energies by umbrella sampling perturbation. J. Comput. Chem. 35(31): 2256-2262 (2014) - [j13]Manuel P. Luitz, Martin Zacharias:
Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials. J. Chem. Inf. Model. 54(6): 1669-1675 (2014) - [j12]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): 221-226 (2014) - 2013
- [j11]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:
Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus. PLoS Comput. Biol. 9(6) (2013) - 2012
- [j10]Piotr Setny, Ranjit Bahadur, Martin Zacharias:
Protein-DNA docking with a coarse-grained force field. BMC Bioinform. 13: 228 (2012) - 2011
- [j9]Simon Leis, Martin Zacharias:
Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J. Comput. Chem. 32(16): 3433-3439 (2011) - [j8]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): 33 (2011) - 2010
- [j7]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: 381 (2010) - 2009
- [j6]Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias:
Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinform. 10: 302 (2009) - [j5]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): 479-492 (2009) - 2002
- [j4]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): 305-311 (2002) - 1999
- [j3]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): 287-300 (1999) - 1995
- [j2]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): 454-464 (1995) - 1990
- [j1]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): 3893-3901 (1990)
Conference and Workshop Papers
- 2001
- [c1]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: 234
Coauthor Index
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