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AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations
No full textWhile accurately modeling the conformational ensemble is required for predicting properties of flexible molecules, the optimal method of obtaining the conformational ensemble appears as varied as their applications. Ensemble structures have been modeled by generation, refinement, and clustering of conformations with a sufficient number of samples. We present a conformational clustering algorithm intended to automate the conformational clustering step through the Louvain algorithm, which requires minimal hyperparameters and importantly no predefined number of clusters or threshold values. The conformational graphs produced by this method for O-succinyl-l-homoserine, oxidized nicotinamide adenine dinucleotide, and 200 representative metabolites each preserved the geometric/energetic correlation expected for points on the potential energy surface. Clustering based on these graphs provides partitions informed by the potential energy surface. Automating conformational clustering in a workflow with AutoGraph may mitigate human biases introduced by guess and check over hyperparameter selection while allowing flexibility to the result by not imposing predefined criteria other than optimizing the model’s loss function
2/17/2021: Course Change Form CS 682
No full textThe change or pre-req from CS 641 Foundations in Data Science to CS 601 Programming Methods for Data Science or BS in CS or Equivalent recognizes that the real content needed for 682 is strong programming skills, rather than the knowledge in 641. The new pre-req parallels the pre-req for the coupled undergraduate version CS 482 which has CS 102 as its pre-req
2/17/2021: Program Change Form Ind & Man Eng
No full textThis proposal aims to create a new concentration within the General Engineering BS program: “Engineering Management”
The differences from the other BSE concentrations include:
1. Replacing MATH 204/305 with IME 332, MATH 350 and a MATH/SCI elective. Rationale: a focus on statistical methods and financial mathematics that are appropriate for engineering management
2. Replacing MECH 311 for a more relevant IME course.
Beyond the core, the concentration includes a mix of IME courses and SoM courses based on the ASEM Book of Knowledge (included at the end of the catalog description for reference).
A few notes:
1. It meets the requirements to submit for ABET accreditation.
2. It contains two free electives which might be needed as pre-reqs, specifically. MGMT 104 for MGMT 205 and BUSN 221 for BUSN 331).
3. The proposal has been discussed with SoM and Dean
We believe this degree will allow us to retain some students that are struggling with higher-level math but will provide them with a very marketable degre
Identification of Individual Components of a Commercial Wheat Germ Acid Phosphatase Preparation
Get PDFWheat germ acid phosphatase (WGAP) is a commercial preparation of partially purified protein commonly used in laboratory settings for non-specific enzymatic dephosphorylation. It is known that these preparations contain multiple phosphatase isozymes and are still relatively crude. This study therefore aimed to identify the protein components of a commercial preparation of wheat germ acid phosphatase using mass spectroscopy and comparative genomics. After one post-purchase purification step, the most prevalent fifteen proteins in the mixture included heat shock proteins, beta-amylases, glucoseribitol dehydrogenases, enolases, and an aminopeptidase. While not among the most abundant components, eight unique dephosphorylation enzymes were also present including three purple acid phosphatases. Furthermore, it is shown that some of these correspond to previously isolated isozymes; one of which has been also previously shown by transcriptome data to be overexpressed in wheat seeds. In summary, this study identified the major components of WGAP including phosphatases and hypothesizes the most active components towards a better understanding of this commonly used laboratory tool
