Martin Zacharias

34 papers Journal 33Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	ParallelKDE.jl: A Package for Highly Parallel Kernel Density Estimation. J. Open Source Softw. Christian Sustay Martinez, Martin Zacharias, Patrick K. Quoika
2024	J	`jnl`	Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations. J. Chem. Inf. Model. Luis J. Walter, Patrick K. Quoika, Martin Zacharias
2023	J	`jnl`	Benchmarking biomolecular force field-based Zn J. Comput. Chem. Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias
2023	J	`jnl`	Mechanism of J. Comput. Chem. Richard L. Zschau, Martin Zacharias
2022	J	`jnl`	Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock. J. Chem. Inf. Model. Maximilian Meixner, Martin Zachmann, Sebastian Metzler, Jonathan Scheerer, Martin Zacharias, Iris Antes
2022	J	`jnl`	Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. J. Comput. Chem. Mateusz Marcisz, Margrethe Gaardløs, Krzysztof K. Bojarski, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov
2021	J	`jnl`	Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling. PLoS Comput. Biol. Danial Pourjafar-Dehkordi, Martin Zacharias
2021	J	`jnl`	Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. J. Comput. Chem. Martyna Maszota-Zieleniak, Mateusz Marcisz, Malgorzata M. Kogut, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov
2021	J	`jnl`	Mechanism of collagen folding propagation studied by Molecular Dynamics simulations. PLoS Comput. Biol. Julian Hartmann, Martin Zacharias
2021	J	`jnl`	Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? J. Chem. Inf. Model. Mateusz Marcisz, Martin Zacharias, Sergey A. Samsonov
2020	J	`jnl`	Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling. J. Chem. Inf. Model. Till Siebenmorgen, Martin Zacharias
2020	J	`jnl`	Prediction of protein-protein complexes using replica exchange with repulsive scaling. J. Comput. Chem. Till Siebenmorgen, Michael Engelhard, Martin Zacharias
2019	J	`jnl`	Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. J. Comput. Chem. Sergey A. Samsonov, Martin Zacharias, Isaure Chauvot de Beauchêne
2017	J	`jnl`	Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. Sjoerd Jacob de Vries, Martin Zacharias
2017	J	`jnl`	The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. Sjoerd Jacob de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry
2017	J	`jnl`	Update of the ATTRACT force field for the prediction of protein-protein binding affinity. J. Comput. Chem. Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci
2016	J	`jnl`	Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. PLoS Comput. Biol. Isaure Chauvot de Beauchêne, Sjoerd Jacob de Vries, Martin Zacharias
2016	J	`jnl`	Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J. Comput. Chem. Maria M. Reif, Martin Zacharias
2014	J	`jnl`	Efficient calculation of relative binding free energies by umbrella sampling perturbation. J. Comput. Chem. Fabian Zeller, Martin Zacharias
2014	J	`jnl`	Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. J. Comput. Chem. Katja Ostermeir, Martin Zacharias
2014	J	`jnl`	PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res. Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy, Pierre Tufféry
2014	J	`jnl`	Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials. J. Chem. Inf. Model. Manuel P. Luitz, Martin Zacharias
2013	J	`jnl`	Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B PLoS Comput. Biol. 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
2012	J	`jnl`	Protein-DNA docking with a coarse-grained force field. BMC Bioinform. Piotr Setny, Ranjit Bahadur, Martin Zacharias
2011	J	`jnl`	Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent. J. Cheminformatics Srinivasaraghavan Kannan, Wolfgang Sippl, Martin Zacharias
2011	J	`jnl`	Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J. Comput. Chem. Simon Leis, Martin Zacharias
2010	J	`jnl`	EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinform. Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang
2009	J	`jnl`	Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping. J. Comput. Chem. Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias
2009	J	`jnl`	Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinform. Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
2002	J	`jnl`	Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2. Silico Biol. Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias
2001	—	`conf`	Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations. German Conference on Bioinformatics Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias
1999	J	`jnl`	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. Martin Zacharias, Heinz Sklenar
1995	J	`jnl`	A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, James Andrew McCammon
1990	J	`jnl`	The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions. Nucleic Acids Res. Günter Theißen, Jürgen Eberle, Martin Zacharias, Luise Tobias, Rolf Wagner