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Ligand binding affinities from MD simulations.
Simplified free energy calculations based on force field energy estimates of ligand-receptor interactions and thermal conformational sampling have emerged as a useful tool in structure-based ligandExpand
Resolving the energy paradox of chaperone/usher-mediated fibre assembly.
Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles of Gram-negative pathogens in a process that has been suggested to be driven by folding energy.Expand
Crystal Structure of the Mobile Metallo-β-Lactamase AIM-1 from Pseudomonas aeruginosa: Insights into Antibiotic Binding and the Role of Gln157
ABSTRACT Metallo-β-lactamase (MBL) genes confer resistance to virtually all β-lactam antibiotics and are rapidly disseminated by mobile genetic elements in Gram-negative bacteria. MBLs belong toExpand
Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm
Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm
Ferric uptake regulator protein: Binding free energy calculations and per‐residue free energy decomposition
Iron homeostasis is, in many bacterial species, mediated by the ferric uptake regulator (Fur). A regulatory site able to bind iron to activate Fur for DNA binding has been described, and a structuralExpand
Free energy calculations and ligand binding.
Publisher Summary This chapter gives an overview of some different methods for calculating ligand binding free energies that are all based on force fields and conformational sampling. Many of theseExpand
Binding affinity prediction with different force fields: Examination of the linear interaction energy method
A systematic study of the linear interaction energy (LIE) method and the possible dependence of its parameterization on the force field and system (receptor binding site). Expand
A synthetic antimicrobial peptidomimetic (LTX 109): stereochemical impact on membrane disruption.
LTX 109 is a synthetic antimicrobial peptidomimetic (SAMP) currently in clinical phase II trials for topical treatment of infections of multiresistant bacterial strains. All possible eightExpand
Antimicrobial peptides with stability toward tryptic degradation.
The inherent instability of peptides toward metabolic degradation is an obstacle on the way toward bringing potential peptide drugs onto the market. Truncation can be one way to increase theExpand
Trypsin specificity as elucidated by LIE calculations, X‐ray structures, and association constant measurements
The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold‐adapted AST has been studied by use of association constant measurements, structural analysisExpand