G
Gerhard Klebe
Researcher at University of Marburg
Publications - 466
Citations - 26140
Gerhard Klebe is an academic researcher from University of Marburg. The author has contributed to research in topics: Ligand (biochemistry) & Isothermal titration calorimetry. The author has an hindex of 69, co-authored 458 publications receiving 24424 citations. Previous affiliations of Gerhard Klebe include Martin Luther University of Halle-Wittenberg & Ludwig Maximilian University of Munich.
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Todd J. Dolinsky,Paul Czodrowski,Hui Li,Jens Erik Nielsen,Jan H. Jensen,Gerhard Klebe,Nathan A. Baker +6 more
TL;DR: The significantly expanded PDB2PQR is reported that includes robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code.
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Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity.
TL;DR: An alternative approach is reported to compute property fields based on similarity indices of drug molecules that have been brought into a common alignment using a Gaussian-type distance dependence, and no singularities occur at the atomic positions.
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Knowledge-based scoring function to predict protein-ligand interactions
TL;DR: The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented and is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK.
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Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.
Holger Gohlke,Gerhard Klebe +1 more
TL;DR: The present review summarizes the current understanding of the binding affinity of a small-molecule ligand to a protein and theoretical and empirical approaches for predicting binding affinity, starting from the three-dimensional structure of a protein-ligand complex, will be described and compared.