Senior Project Advisor
PDZ Domains, Biology, Computer Science, Bioinformatics, Proteins
Studies of protein mutants in wet laboratory experiments are expensive and time consuming. Computational experiments that simulate the motions of protein with amino acid substitutions can complement wet lab experiments for studying the effects of mutations. In this work we present a computational pipeline that performs exhaustive single-point amino acid substitutions in silico. We perform energy minimization as part of molecular dynamics (MD) of our generated mutant proteins, and the wild type, and log the energy potentials for each step of the simulations. We motivate several metrics that rely on the energy minimization curves of the wild type and mutant, to explore quantitatively the effects of the mutations. Two case studies are discussed and analyzed to showcase the utility of our approach to identify the least and most impactful mutations.
Index Terms—Energy minimization, mutation, computational biochemistry, structural biology
Lee, Matthew; Van Roy, Bodi; and Jagodzinski, Filip, "Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline" (2020). WWU Honors College Senior Projects. 551.
Subjects - Topical (LCSH)
Computational biology; Molecular dynamics; Mutation (Biology); Proteins--Biotechnology
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