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Showing 1 to 20 of 25 for “"protein-ligand binding"”.
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Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities
Biological processes often depend on protein-ligand binding events, so that accurate prediction of protein-ligand binding affinities is of central importance in structural based drug design. Although many techniques exist for calculating protein-ligand binding affinities, ranging from techniques …
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Protein-Ligand Binding Affinity Directed Multi-Objective Drug Design Based on Fragment Representation Methods
… by fragment-based drug search for a given protein target and the emergence of artificial intelligence (AI) approaches in this field, this work advances the field of in silico drug design by (1) integrating a graph fragmentation-based deep generative model with a deep evolutionary learning …
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Design, synthesis, and thermodynamic evaluation of peptidomimetic ligands binding to the Src SH2 domain
The ability to predict protein-ligand binding affinities is a difficult and elusive goal in the field of molecular recognition. Models exist to predict binding energetics; however, they are not always capable of considering the incidental events in ligand-binding due to the tendency of the Gibbs …
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Efficient Biomolecular Computations Towards Applications in Drug Discovery
… of this research is to improve the accuracy of protein-ligand binding calculations in the implicit solvent framework. To address the problem (1) GBNSR6, an accurate yet efficient flavor of GB, has been thoroughly explored in the context of protein-ligand binding, (2) a global multidimensional …
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Revisiting and re-computing the X-score scoring function
… functions seek to compute in different ways protein-ligand binding energies by summing together the individual pairwise atomic interaction energies observed in crystal structures between the protein and the bound ligand. To date though, accurate prediction remains a big challenge since …
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Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
… models to analyze the molecular basis of binding affinity in the context of protein-protein and protein-ligand binding as well as reaction rate enhancement in enzyme catalysis. First, we evaluate the solvent screened energetics of immunoglobulin G (IgG):Fc[gamma] receptor binding using …
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Novel methods in computational analysis and design of protein-protein interactions : applications to phosphoregulated interactions
… methods for the analysis and design of protein-protein complexes, and their application to the study of the interactions of phosphopeptides with phosphopeptide-binding domain interactions. A novel protein-protein interaction type, the action-at-a-distance interaction, is described in the …
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Exploring Protein-Ligand Interaction with Rotamer-Library Based Refinement Tools
… extensively used for the predicting and refining protein sidechains, loops and tertiary structures. These refinement techniques have been expanded to allow the inclusion of protein-ligand interactions by developing and evaluating methods for creating rotamer libraries for small drug-like …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
The cellular function of proteins, and their targeting by drug applications, are both governed by biomolecular thermodynamics and kinetics. In order to make meaningful and efficient predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of …
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The use of terahertz spectroscopy for biomolecular analysis
… the spectra of macromolecules, such as protein and DNA, can reveal information regarding conformation and dynamics. However, terahertz spectroscopy has habitually been underutilised as an investigative tool in biochemistry due to lack of terahertz sources and the strong absorbance of …
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Computational Ligand-Based CNS Therapeutic Design: The Search for Novel-Scaffold Norepinephrine Transporter Inhibitors
Monoamine transporter (MAT) proteins are responsible for regulating cellular signal transduction through control of neurotransmitter reuptake in the synapse, and are therefore relevant to diseases including addiction, psychosis, anxiety and depression. MATs, specifically the serotonin transporter …
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Ubiquitin Conformational Dynamics and Hydration Shell Dynamics by Solid State NMR
Knowledge of protein dynamics is essential for understanding the enzyme catalysis, protein molecular recognition, and the entropy changes during protein-ligand binding. Nuclear Magnetic Resonance (NMR) is an ideal biophysical experimental tool for the study of protein dynamics because it can be …
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Structural basis for the function of the transcriptional regulator KstR from Mycobacterium tuberculosis
… The interactions between KstR and cognate DNA or ligands have been investigated by multiple biochemical techniques (i.e. electrophoretic mobility shift assay, surface plasmon resonance and intrinsic fluorescence quenching assay). Protein-DNA binding assays have demonstrated that the 21-amino-acid …
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The SSIP approach to solvation
… governing many processes, including solvation, protein ligand binding and crystallisation. Previously in the Hunter group, the Surface Site Interaction Point (SSIP) model of intermolecular interactions has been used to describe molecules as a set of discrete hydrogen bonding sites. In this …
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Improving protein docking with binding site prediction
Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, …
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Detection and analysis of binding sites and protein-ligand interactions
Detection and analysis of protein-ligand binding sites is an important area of research in drug discovery. The FTMap web server is an established computational method for detection of binding hot spots, or regions on the protein surface that contribute disproportionately to the ligand binding free …
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Cytoplasmic sensing by Bacillus subtilis chemoreceptors
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo terms
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Regulating the stabilities of NOD1 and NOD2, two innate immune receptors, with sugars and chaperones
… Two well characterizes PRRs are nucleotide- binding oligomerization domain containing proteins 1 and 2 (NOD1 and NOD2), members of the NOD-like receptor family (NLRs). These NLRs recognize different fragments from bacterial cell wall peptidoglycan (PG) using their C-terminal leucine rich …
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A structural classification of protein-protein interactions for detection of convergently evolved motifs and for prediction of protein binding sites on sequence level
… era of Bioinformatics is the prediction of protein-protein interactions, and ultimately the prediction of protein functions. The problem is intrinsically harder, when only amino acid sequences are available, but a solution is more universally applicable. So far, the problem of uncovering …
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Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of …
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