Prof. Sanchez-Garcia's field of research is computational chemistry and computational chemical biology, with emphasis on complex biological systems, solvent effects and reactive intermediates. Before she established the Group of Computational Biochemistry within the Faculty of Biology of the University of Duisburg-Essen, she was independent group leader at the Theory Department directed by Prof. Walter Thiel in the Max Planck Institute for Coal Research (Mülheim an der Ruhr). At the UDE, the Computational Biochemistry group works on investigating the properties, reactive behavior and applications of diverse systems, from reactive species to protein complexes. Among our main interests are the in silico design of ligands with therapeutic potential and the regulation of enzymatic activity and protein-protein interactions by means of computational mutagenesis, ligands and solvents. Implementation and application of novel computational tools are central to the research.
Dr. Joel Mieres Perez
My work is related to the theoretical study of biomolecules with potential therapeutic activity. The goal is to get new insights on such systems for the in-silico design of ligands with tailor-made properties. In addition, I investigate the spectroscopic behavior and chemical reactivity of organic molecules, to predict reaction pathways which can be then tested by the experimentalists. I also work on systems where quantum tunneling plays a key role and develop theoretical approaches for the prediction of tunneling probabilities.
Dr. Yasser B. Ruiz Blanco
Google Scholar Profile
Dr. Ruiz-Blanco, Y.B. is an experienced researcher applying machine learning (ML) approaches in Bioinformatics. Dr. Ruiz-Blanco devised numerical encodings protocols for proteins (ProtDCal), which have been successfully applied to build predictive ML-based models of protein-protein interactions, post-translational modifications, and the identification of anti-bacterial peptides (ProtDCal-Suite). In addition, he possesses a wide knowledge about advanced molecular simulation methods. Together with Prof. Sanchez-Garcia he developed CL-FEP, an unbiased end-state free energy change estimator based on the FEP equation and the central limit theorem. Dr. Ruiz-Blanco's research combines computational chemistry methods and artificial intelligence in the development of efficient computational approaches for molecular design and drug discovery processes.
Dr. Pradeep Pant
My research work focuses on elucidating the role of solvent as a function of pH to gather insights into the conformational and functional adaptations of biomacromolecular systems using advanced MD simulations, hybrid QM/MM techniques and free energy perturbation calculations. This will help in delineating the mechanism as how the rigidity/flexibility associated with polypeptide chains influence the resultant structure of a macromolecule, which in turn dictates the function of a macromolecule upon varying the pH of a solution.
Dr. Yasser Almeida Hernández
I am experienced in the structural experimental and computational characterization of proteins. My current work is focused on the design and application of new multiscale approaches to model biomolecular systems. I am particularly interested in the application of hybrid coarse-graining approaches to study reaction mechanisms, solvation, and protein folding. The final goal is to improve the computational performance of molecular dynamics simulations and prediction algorithms while achieving an accurate structural and thermodynamic description of large biomolecular systems.
MSc. Sandra Romero Molina
My research is focused in Bioinformatics. My main interest is to develop integrated methodologies combining novel machine-learning-based predictors and computational chemistry methods. Particularly, I am involved in the development of protein-protein interaction models, with application for the de novo design of bioactive peptides and as scoring function for docking algorithms.
Julio C. Vieyto Nuñez
A big area of interest for me is biomolecular modelling using state-of-the-art approaches in molecular dynamics simulations and hybrid techniques. My research is mainly focused on the computational study of supramolecular ligands on proteins; which includes ligand binding sites prediction and binding free energy calculations as well as molecular docking oriented to in silico drug design. I am also interested in the study of the influence of different solvent mixtures on enzymatic reactions and protein properties.
M.Sc. Mazlum Budak
I am very interested in the field of enzymatic reactions and bio-organic chemistry. My research mainly focuses on the computational design and development of bioactive molecules/peptides for protein inhibition via docking calculations and advanced molecular dynamics simulations. In addition, I am also engaged in unravelling reaction mechanisms via quantum mechanics.
Julia Wille, University of Ulm (November 2019)
Dr. Matthias Heyden, Arizona State University (June-July 2018)
Dr. Sunil Kumar Tripathi (2019 -2020)
Dr. Jörg Tatchen (2017 - 2020)
Dr. Kenny Bravo-Rodriguez (2011 - 2019)
Dr. Angela Rodriguez Serrano (2017 - 2019)
Dr. Pandian Sokkar (2013 - 2018)
Dr. Sumit Mittal (2013 - 2018)
Amandeep Singh (internship 2018)
Figures generated using the VMD software. VMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.
Humphrey, W., Dalke, A. and Schulten, K., `VMD -Visual Molecular Dynamics, J. Molecular Graphics, 1996, vol. 14, pp. 33-38.http://www.ks.uiuc.edu/Research/vmd/