Matching Items (4)
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- All Subjects: MATLAB
- Creators: Trichopoulos, Georgios
- Creators: Woodbury, Neal
Description
Predicting the binding sites of proteins has historically relied on the determination of protein structural data. However, the ability to utilize binding data obtained from a simple assay and computationally make the same predictions using only sequence information would be more efficient, both in time and resources. The purpose of this study was to evaluate the effectiveness of an algorithm developed to predict regions of high-binding on proteins as it applies to determining the regions of interaction between binding partners. This approach was applied to tumor necrosis factor alpha (TNFα), its receptor TNFR2, programmed cell death protein-1 (PD-1), and one of its ligand PD-L1. The algorithms applied accurately predicted the binding region between TNFα and TNFR2 in which the interacting residues are sequential on TNFα, however failed to predict discontinuous regions of binding as accurately. The interface of PD-1 and PD-L1 contained continuous residues interacting with each other, however this region was predicted to bind weaker than the regions on the external portions of the molecules. Limitations of this approach include use of a linear search window (resulting in inability to predict discontinuous binding residues), and the use of proteins with unnaturally exposed regions, in the case of PD-1 and PD-L1 (resulting in observed interactions which would not occur normally). However, this method was overall very effective in utilizing the available information to make accurate predictions. The use of the microarray to obtain binding information and a computer algorithm to analyze is a versatile tool capable of being adapted to refine accuracy.
ContributorsBrooks, Meilia Catherine (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Ghirlanda, Giovanna (Committee member) / Department of Psychology (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The field of biomedical research relies on the knowledge of binding interactions between various proteins of interest to create novel molecular targets for therapeutic purposes. While many of these interactions remain a mystery, knowledge of these properties and interactions could have significant medical applications in terms of understanding cell signaling and immunological defenses. Furthermore, there is evidence that machine learning and peptide microarrays can be used to make reliable predictions of where proteins could interact with each other without the definitive knowledge of the interactions. In this case, a neural network was used to predict the unknown binding interactions of TNFR2 onto LT-ɑ and TRAF2, and PD-L1 onto CD80, based off of the binding data from a sampling of protein-peptide interactions on a microarray. The accuracy and reliability of these predictions would rely on future research to confirm the interactions of these proteins, but the knowledge from these methods and predictions could have a future impact with regards to rational and structure-based drug design.
ContributorsPoweleit, Andrew Michael (Author) / Woodbury, Neal (Thesis director) / Diehnelt, Chris (Committee member) / Chiu, Po-Lin (Committee member) / School of Molecular Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This Creative Project was carried out in coordination with the capstone project, Around the Corner Imaging with Terahertz Waves. This capstone project deals with a system designed to implement Around the Corner, or Non Line-of-Sight (NLoS) Imaging. This document discusses the creation of a GUI using MATLAB to control the Terahertz Imaging system. The GUI was developed in response to a need for synchronization, ease of operation, easy parameter modification, and data management. Along the way, many design decisions were made ranging from choosing a software platform to determining how variables should be passed. These decisions and considerations are discussed in this document. The resulting GUI has measured up to the design criteria and will be able to be used by anyone wishing to use the Terahertz Imaging System for further research in the field of Around the Corner or NLoS Imaging.
ContributorsWood, Jacob Cannon (Author) / Trichopoulos, Georgios (Thesis director) / Aberle, James (Committee member) / Electrical Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The purpose of this project is to analyze the MIT OpenCourseWare coffee can radar design and modify it to be better suited for drone based synthetic aperture radar (SAR) applications while maintaining the low-cost aspect of the original design. The MIT coffee can radar can function as a ranged radar, a Doppler radar, or as SAR. Through simulations and research, the suggestions for how to modify the radar resulted in swapping the coffee can monopole antennas for patch antenna arrays or helical ordinary end-fire antennas, adding an Arduino for automatic recording of output pulses, and switching from a breadboard construction to a PCB to shrink form factor and keep costs and construction time low.
ContributorsRivera, Danielle (Author) / Trichopoulos, Georgios (Thesis director) / Aberle, James (Committee member) / Department of Information Systems (Contributor) / Electrical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12