L
Lada Biedermannová
Researcher at Academy of Sciences of the Czech Republic
Publications - 24
Citations - 1719
Lada Biedermannová is an academic researcher from Academy of Sciences of the Czech Republic. The author has contributed to research in topics: Protein structure & Virtual screening. The author has an hindex of 11, co-authored 21 publications receiving 1409 citations. Previous affiliations of Lada Biedermannová include University of Glasgow & Masaryk University.
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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Eva Chovancová,Antonín Pavelka,Petr Beneš,Ondrej Strnad,Jan Brezovsky,Barbora Kozlíková,Artur Góra,Vilém Šustr,Martin Klvana,Petr Medek,Lada Biedermannová,Jiri Sochor,Jiri Damborsky +12 more
TL;DR: A new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations is presented, and analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating.
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MedusaScore: an accurate force field-based scoring function for virtual drug screening.
TL;DR: In this paper, a novel scoring function, MedusaScore, was proposed for evaluating protein-ligand binding, which is based on models of physical interactions that include van der Waals, solvation, and hydrogen bonding energies.
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On the Mechanism of Asymmetric Allylation of Aldehydes with Allyltrichlorosilanes Catalyzed by QUINOX, a Chiral Isoquinoline N-Oxide
Andrei V. Malkov,Pedro Ramírez-López,Lada Biedermannová,Lubomír Rulíšek,Lenka Dufkova,Martin Kotora,Fujiang Zhu,Pavel Kocovsky +7 more
TL;DR: A good agreement between the theoretically predicted enantioselectivities for 1a and 1h and the experimental data allowed to understand the specific aspects of the reaction mechanism, and it is suggested that attractive aromatic interactions between the catalyst 9 and the aldehyde 1 contribute to the enantiodifferentiation.
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Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane
TL;DR: The strength of proline non-covalent interactions, combined with this residue's rigidity, might be the explanation for its prominent role in protein stabilization and recognition processes.
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Software tools for identification, visualization and analysis of protein tunnels and channels.
TL;DR: A review of software tools specialized in rapid identification, visualization, analysis and design of protein tunnels and channels can be found in this article, along with examples of their applications for the analysis and engineering of various biological systems.