Browsing Τμήμα Φυσικής / Department of Physics by Subject "Ligands"
Now showing items 1-10 of 10
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Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase
(2011)Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...
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Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin
(2011)The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive ...
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Free energy simulations come of age: Protein-ligand recognition
(2002)In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
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Free energy simulations: The meaning of the individual contributions from a component analysis
(1994)A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred ...
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Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues
(2005)GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could ...
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Lead halide perovskites and other metal halide complexes as inorganic capping ligands for colloidal nanocrystals
(2014)Lead halide perovskites (CH3NH3PbX3, where X = I, Br) and other metal halide complexes (MXn, where M = Pb, Cd, In, Zn, Fe, Bi, Sb) have been studied as inorganic capping ligands for colloidal nanocrystals. We present the ...
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Article
Proteus and the design of ligand binding sites
(2016)This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...
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Recognition of ribonuclease A by 3′-5′-pyrophosphate-linked dinucleotide inhibitors: A molecular dynamics/continuum electrostatics analysis
(2007)The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic ...
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Single crystal coordinating solvent exchange as a general method for the enhancement of the photoluminescence properties of lanthanide MOFsAAA
(2014)The discovery of new methods for the post-synthesis modification of materials is essential in order to establish suitable strategies for the tuning of their properties in a rational manner. Here we present a series of ...
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Structural and electronic properties of bare and capped Cd nSe n/Cd nTe n Nanoparticles (n = 6, 9)
(2012)Relationships between structures and properties (energy gaps, vertical ionization potentials (IP v), vertical electron affinities (EA v), and ligand binding energies) in small capped CdSe/CdTe nanoparticles (NPs) are poorly ...