Martin Zacharias
Orcid: 0000-0001-5163-2663
According to our database1,
Martin Zacharias
authored at least 33 papers
between 1990 and 2024.
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Bibliography
2024
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations.
J. Chem. Inf. Model., 2024
2023
J. Comput. Chem., 2023
Benchmarking biomolecular force field-based Zn<sup>2+</sup> for mono- and bimetallic ligand binding sites.
J. Comput. Chem., 2023
2022
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock.
J. Chem. Inf. Model., 2022
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes.
J. Comput. Chem., 2022
2021
Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling.
PLoS Comput. Biol., 2021
PLoS Comput. Biol., 2021
J. Chem. Inf. Model., 2021
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans.
J. Comput. Chem., 2021
2020
Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling.
J. Chem. Inf. Model., 2020
Prediction of protein-protein complexes using replica exchange with repulsive scaling.
J. Comput. Chem., 2020
2019
J. Comput. Chem., 2019
2017
Nucleic Acids Res., 2017
Fast and accurate grid representations for atom-based docking with partner flexibility.
J. Comput. Chem., 2017
Update of the ATTRACT force field for the prediction of protein-protein binding affinity.
J. Comput. Chem., 2017
2016
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.
PLoS Comput. Biol., 2016
Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules.
J. Comput. Chem., 2016
2014
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Nucleic Acids Res., 2014
Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials.
J. Chem. Inf. Model., 2014
Efficient calculation of relative binding free energies by umbrella sampling perturbation.
J. Comput. Chem., 2014
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.
J. Comput. Chem., 2014
2013
Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B <i>Streptococcus</i>.
PLoS Comput. Biol., 2013
2012
2011
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent.
J. Cheminformatics, 2011
J. Comput. Chem., 2011
2010
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results.
BMC Bioinform., 2010
2009
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.
J. Comput. Chem., 2009
BMC Bioinform., 2009
2002
Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2.
Silico Biol., 2002
2001
Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001
1999
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., 1999
1995
J. Comput. Chem., 1995
1990
The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions.
Nucleic Acids Res., 1990