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AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions
(Oxford University Press, 2019-10)
Summary: The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand ...
Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening
(American Chemical Society, 2019-08)
Virtual screening of large compound databases, looking for potential ligands of a target protein, is a major tool in computer-aided drug discovery. Throughout the years, different techniques such as similarity searching, ...
WATCLUST: a tool for improving the design of drugs based on protein-water interactions
(Oxford University Press, 2015-05)
Motivation: Water molecules are key players for protein folding and function. On the protein surface, water is not placed randomly, but display instead a particular structure evidenced by the presence of specific water ...
Solvent structure improves docking prediction in lectin-carbohydrate complexes
(Oxford University Press, 2013-02)
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but ...
An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein-monosaccharide complexes
(Oxford University Press, 2018-11)
Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging ...
Evaluación de un candidato a transportador de NAD+ en el parásito protozoario Trypanosoma cruzi
(Universidad Nacional de ColombiaBogotá - Ciencias - Maestría en Ciencias - BioquímicaDepartamento de QuímicaFacultad de CienciasBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá, 2021)
Trypanosoma cruzi causa la enfermedad de Chagas, patología distribuida globalmente y carente de tratamientos efectivos, lo que hace pertinente la búsqueda de estrategias alternas de control. La dinámica del dinucleótido ...