Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 27 for “"Binding free energy"”.
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Optimization of electrostatic binding free energy : application to barnase and barstar
Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Physics, 1999.
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Molecular mechanism, binding free energy, and sequence selectivity of intercalation of doxorubicin and DNA
… interact noncovalently with DNA either by groove binding or intercalation. Intercalation is a key process in drug discovery and biosensor development. Doxorubicin (DOX) is an intercalator drug that treats a wide range of cancers. However, its binding process with DNA is still a highly debatable …
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Optimization of electrostatic binding free energy : applications to the analysis and design of ligand binding in protein complexes
… distribution which optimizes the electrostatic binding free energy - the electrostatic complement of the target receptor. This electrostatic affinity optimization procedure was applied to several systems both in order to understand the role of electrostatic interactions in natural systems and as …
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Insights into the Substrate Binding Specificity of Quorum-Quenching Acylase PVDQ
… lengths and substituents. However, the substrate binding specificity determinants of PvdQ with different bacterial ligands remain unknown and unintuitive. Elucidation of these determinants can lead to mutants with efficiency and broader substrate promiscuity. To investigate this question, a …
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Thermodynamics of Ligand Binding to Glutamate Dehydrogenase
… of the mechanism of allosteric ligand binding to GDH. During our computational investigation, we discovered a 40-year-old sequence error at the NADH/ADP/ECG binding site. Residue 387 was mistakenly identified as asparagine rather than the correct amino acid identity, lysine. The free …
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Applications of Funneled Landscapes: Protein Folding and Molecular Recognition
Energy landscape theory provides a general framework in which models can be used to describe complex macromolecular processes. A free energy functional model is formulated to describe protein folding which includes a specific potential, a polymer chain entropy, and explicit physically motivated …
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Efficient Methods for Exploring Chemical Space in Computational Drug Discovery
… in chapter 2, is for the application of free energy methods to the problem of computational fluorine scanning. The application made in this work will allow for all fluorinated analogues of a compound to be tested five times faster than existing computational methods and with comparable …
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Protein design with hierarchical treatment of solvation and electrostatics
A detailed treatment of the electrostatic energy of biomolecules in solution is used for two applications that require consideration of large numbers of states: multiple-site titration and protein design. The continuum electrostatic model is combined with covalent, van der Waals, and non-polar …
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Computational structure-based modeling and analysis with application to rational and evolutionary molecular engineering
… improves the electrostatic component of the binding free energy, despite changes in binding mode and discrete chemical constraints. Additionally, chemical changes suggested by charge optimization frequently corresponded to tighter-binding inhibitors, indicating that this technique would be …
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A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods
… this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… simulations must be able to estimate the binding affinity and rates of association and dissociation of a protein-ligand complex, or the populations and rates of exchange between distinct conformational states (i.e. folding and unfolding, binding and unbinding). The above studies are …
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Analysis of the biophysical and in silico exploration of the interaction between small ribonucleoprotein G and the RING finger domain of retinoblastoma binding protein 6 for the identification of protein anti-cancer compounds
… to as SmG in this study) and retinoblastoma binding protein 6 (RBBP6), which have been identified as potential diagnostic markers for cancer treatment. The broad focus of this study was to investigate the putative interactions between these two proteins. In-silico analysis and …
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Toward therapeutic nanoassemblies: the design and modeling of protein-protein interactions.
… While initial attempts at calculating the binding free energy of the macromolecular complex have been unsuccessful, we have gleaned important insights into the complexities of modeling this three-body system. The advances described within the following work delineate important aspects of …
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Computer-aided design and synthesis of 5,7-dihydroxyflavone derivatives as glycogen phosphorylase inhibitors
… as molecular docking with Glide and post-docking binding free energy calculations using advanced QM/MM-PBSA calculations, we have screened a large library of 1239 5,7-dihydroxyflavone analogues which have the potential to bind at the inhibitor site of glycogen phosphorylase. We compared these …
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Study of macromolecular interactions using computational solvent mapping
The term "binding hot spots" refers to regions of a protein surface with large contributions to the binding free energy. Computational solvent mapping serves as an analog to the major experimental techniques developed for the identification of such hot spots using X-ray and nuclear magnetic …
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Computational modeling of protein-protein and protein-peptide interactions
… near-native docking results and changes in binding free energy is established, and used to investigate changes in binding affinity following mutation across two antibody-antigen systems: influenza and anthrax. The second project demonstrates that a motif-based search of available protein …
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The Cocaine-Binding Aptamer: A Thermodynamic and Structural Overview of Specific and Non-Specific Binding Interactions
… wherein variances in the heat capacity of binding (Cp) among variants of the cocaine-binding aptamer were suggestive of two distinct binding mechanisms. Aptamer variants containing 6 base pairs in stem 1 are pre-folded and show little change in secondary structure with ligand binding. …
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Protein-ligand interaction studies and identification of new drug-like hits as cannabinoid receptor modulators
… including: (1) an examination of the putative binding modes of Cannabis-derived ligands with CB1 and CB2 receptors, (2) the identification of novel CB1 inverse agonists, and (3) the identification of allosteric site(s) in the CB2 receptor and screening of new CB2 allosteric modulators …
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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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ScRING finger protein, Mdm2, MdmX, p53, cancer, ubiquitination, drug discovery, ZINC16046951, University of Zululand, South Africa
… out amongst others as it lacked the first zinc binding site which is abnormal for RING finger domain (Kappo et al., 2012). ScRING finger domain is cysteine rich domain from a Mpe-1 RBBP6 homologue that binds zinc ion for structural stability. Therefore, biochemical, structural and In silico …
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