Jeffrey L Mills's research while affiliated with Rochester Institute of Technology and other places
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Publications (14)
This curriculum from the BASIL (Biochemistry Authentic Scientific Inquiry Laboratory) biochemistry consortium aims to get students to transition from thinking like students to thinking like scientists. Students will analyze proteins with known structure but unknown function using computational analyses and wet-lab techniques. BASIL is designed for...
Students at the Rochester Institute of Technology and Dowling College used bioinformatics software, which they had helped develop, to predict the function of protein structures whose functions had not been assigned or confirmed. Over the course of time, they incorporated other bioinformatics tools and moved the project to the wet lab, where they so...
Interdisciplinary collaborations are often essential to answer multi-faceted questions, yet they present with many challenges such as understanding the information, methodologies, and norms of another field and effective communication between team members. We must begin to provide young scientists with the skills necessary for success as the call f...
The need for a significant improvement in undergraduate STEM education has been broadly recognized. We have designed and implemented a research-driven curriculum for undergraduate biochemistry labs. The primary purposes of this project are to (1) improve understanding of the process of training students to be effective scientists, (2) test the hypo...
It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for in silico prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins “of unknown function” in the P...
Copper(i) N-heterocyclic carbene (CuNHC) complexes are more catalytically active than traditional transition metal salts for the cyclopropenation of internal alkynylsilanes and diazoacetate compounds. A series of 1,2,3-trisubstituted and 1,2,3,3-tetrasubstituted cyclopropenylsilane compounds were isolated in good overall yields. An interesting regi...
ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of p...
Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500...
Citations
... The 3D structures of the pilins and the spatial distribution of the residues were visualized using PyMOL software [42,43]. The percentage of residues was measured using the amino acid composition module in BioEdit package [44]. ...
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... In the current study, we adopt this approach to investigate student perceptions for specific course-based undergraduate research abilities that were identified in previous studies using the process for identifying course-based undergraduate research abilities (PICURA) 3,4 as the anticipated learning outcomes (ALOs) or course-based undergraduate research abilities (CURAs) for the BASIL CURE. 5,10 In this regard, as stated in our previous papers, 3,4 it is important to emphasize that knowledge of the biochemistry subject matter, as well as basic procedural (technical) knowledge, is important prerequisite knowledge for mastering these CURAs. However, in the current study we considered it unnecessary to construct ALO statements for everything that students needed to know, as ultimately lack of such basic knowledge would be revealed in student assessment of the CURAs. ...
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... For example, they have been found to be beneficial in summer research programs for underrepresented students (3)(4)(5)(6)(7). Other institutions that have used them throughout the academic year have found that they helped with student engagement and persistence (8)(9)(10)(11). Over the course of their academic careers, students ...
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... In 2016, a Cu(I)/N-heterocyclic carbene (CuNHC) complex catalyzed cyclopropenation of internal alkynylsilanes 113 with diazoacetate 15 was reported by Coleman's group [147]. A series of 1,2,3-trisubstituted and 1,2,3,3-tetrasubstituted cyclopropenylsilane compounds 114 were isolated in moderate to good yields (Scheme 30). ...
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... In multiple alignment analysis, three basic amino acids (Lys 37, 44 and Arg 70 ) and six acidic amino acids (Asp 6,45,48,51,60 and Glu 41 ) are conserved in PYDs of DrNLRP3 and DrCaspase-A. Furthermore, 11 basic amino acids (Lys 17,28,39,44,73 and Arg 21,37,46,70,77,80 ) and 11 acidic amino acids (Asp 6,45,48,51,60 and Glu 9,13,15,39,41,82 ) are conserved in PYDs of DrNLRP3 and DrCaspase-B (Fig. S1D). ...
... As of March 2020, a total of 17,929 domains were deposited in the Pfam database, with 5792 domains (32% of the total) containing the keyword "unknown function" [18]. Reports indicate that a large fraction of Protein Data Bank (PDB) entries are categorized under "unknown functions" [19,20]. PUFs are common even in well-studied species. ...
