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Full-Text Articles in Physical Sciences and Mathematics
Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor
Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor
Honors Theses
Molecular dynamics (MD) simulations and computational chemistry allow for an atomistic understanding of protein-protein and protein-ligand binding motifs. Through the use of MD, medicinally relevant complexes can be examined in detail unattainable by experimental methods. Within this work, systems pertinent to both Alzheimer’s Disease and HIV-1 are probed and thoroughly sampled to help elucidate potential therapeutic pathways. We used molecular dynamics and free energy estimations to gauge the affinity for the binary and ternary complexes of KLC1, APP and JIP1, three proteins all believed to be involved in the propagation of Alzheimer’s Disease. Two areas of thought exist suggesting that …
Method For Identification Of Origins Of Replication And Genes Regulated By Dnaa In Bacteria, Olga G. Troyanskaya
Method For Identification Of Origins Of Replication And Genes Regulated By Dnaa In Bacteria, Olga G. Troyanskaya
Honors Theses
The study is focused on developing computer programs to identify origin of DNA replication based on analysis of total bacterial genomes, scoring regions for number of DnaA binding sites, AT content, DNA adenine methylase boxes, and integration host factors binding sites. The programs were tested on cyanobacterium Synechocystis, and several potential origins were identified. However, no one definite region could be located. Currently, software is being developed to analyze common motifs around the origins of all bacteria with known origins. Genes whose transcription could be regulated by DnaA were identified by searching for DnaA boxes preceding promoter regions.