Our Community

Explore the following sections to see our community's impact, collaboration, and other highlights.

Computational Resources Developed as Part of Clark Lab Projects

  • %MinMax: Analyze relative codon usage frequencies along a gene of interest
    Originally developed in 2008 (Clarke & Clark, 2008), with an expanded description published in 2018 (Rodriguez et al., 2018). A flexible online server to analyze the extent to which amino acids in a protein sequence is encoded by relatively rare versus common synonymous codons, relative to the codon usage frequencies for the other synonymous codons encoding each amino acid. Output is averaged over a sliding window of codons.
  • CHARMING: Harmonize synonymous codon usage in your gene of interest to match the codon usage frequencies of a host organism
    An open-access online tool to aid with the development of alternative synonymous coding sequences to enhance gene expression (Wright et al., 2021). The algorithm iteratively adjusts synonymous codon usage for an input gene sequence from the codon usage bias of one organism to another.

Other Computational Resources We Frequently Use

  • SAXSonIDPs: Fit SAXS data using a molecular form factor (MFF)
    Developed in 2017 (Riback et al., 2017), with an expanded performance description in 2019 (Riback et al., 2019), the MFF enables accurate interpretation of small angle X-ray scattering (SAXS) data for disordered protein ensembles. The user-friendly online server enables users to upload SAXS data and determine the extent of collapse of a protein using a fitting procedure that returns both the radius of gyration (Rg) and the Flory exponent (n), an estimate of solvent quality.
  • Clustal Omega: Align multiple protein or nucleic acid sequences
    This free online tool developed by EMBL-EBI allows users to compare biomolecule sequences of interest and generate alignments.
  • MEGAX: Generate sequence alignments and phylogenetic trees
    MEGA software was first developed in 1994 (Kumar et al. 1994) for molecular evolutionary genetics analysis. Subsequent updates include the MEGAX version (Kumar et al. 2018), which we use for multiple sequence alignments and phylogenetic analysis of related protein sequences.
  • FPbase: Database for fluorescent proteins
    FPbase (Lambert et al. 2019) is an open-source database for information about fluorescent proteins and their properties.
  • NEB Tm calculator: Melting temperature calculator
    This free online tool from New England Biolabs calculates accurate melting temperatures for primers used in PCR reactions.

Conferences We Frequently Attend

Annual Midwest Conference on Protein Folding, Assembly & Molecular Motions

Founded by Patricia in 2005 and held at Notre Dame each Spring, the Annual Midwest Conference on Protein Folding, Assembly & Molecular Motions is a one-day meeting that brings together Midwest research laboratories interested in protein folding, aggregation, binding, and dynamics. In addition to two keynote lectures, this regional conference provides graduate students, postdocs and other early career researchers with opportunities to present their research and interact with students and faculty in related fields at other institutions. The conference has nucleated several new research collaborations. In addition to the keynote lectures, the program includes ~10 short talks from selected abstracts and a dynamic poster session.

Annual Midwest Conference on the Stress Response & Molecular Chaperones

Hosted at Northwestern University each January by Rick Morimoto, since 1995, the Annual Midwest Conference on the Stress Response & Molecular Chaperones inspired Patricia’s founding of the Midwest Protein Folding conference; the formats are very similar. The primary focus of MWStress is heat shock and molecular chaperones, however other topics of interest include protein aggregation, structure and folding.

Gibbs Conference on Biothermodynamics

An annual conference organized by the Gibbs Society of Biological Thermodynamics. The Gibbs Society was established in 1987 to advance the development and application of thermodynamic principles to understand biological systems. The Gibbs Conference on Biothermodynamics brings together ~250 scientists to discuss recent advances in biothermodynamics, through talks, posters, and informal networking in a rural setting. The conference is committed to offering significant opportunities for oral presentations by early career trainees.

Biophysical Society Annual Meeting

The Biophysical Society was founded in 1958 to lead the development and dissemination of knowledge in biophysics. The Society’s annual meeting brings together >5,000 scientists, researchers, and educators from various disciplines within biophysics. The event features a wide range of activities, including scientific sessions, keynote lectures, poster sessions, workshops, tutorials, networking opportunities, career development programming and exhibits. The conference typically attracts a diverse international audience. Society membership will pay for itself in registration savings and potential travel awards for trainees who attend the Annual Meeting.

Protein Society Annual Symposium

The Protein Society is a not-for-profit professional association for researchers focused on protein structure, function, and design. It was established in 1985. The Society sponsors many workshops, networking opportunities, and publishes Protein Science. The Protein Society annual symposium brings together ~1,000 attendees, including many from outside the US, and many from pharmaceutical and biotechnology companies. Society membership will pay for itself in registration savings and potential travel awards for trainees who attend the Annual Symposium.

Notre Dame Graduate Student Organizations

Notre Dame Graduate Student Government (GSG)

The Notre Dame Graduate Student Government aims to enhance the quality of life for graduate students at the University by improving their educational experience. Key initiatives include providing conference travel grants, highlighting graduate research through the Graduate Research Symposium, advocating for student needs with university administration, encouraging interdisciplinary connections through social events, organizing free and subsidized activities on and off campus, and promoting engagement with the South Bend community. The GSG encourages suggestions from members to better meet the needs of all students and invites active participation.

Chemistry Grad Student Organization (CGSO)

Accredited through the American Chemical Society, the Chemistry Grad Student Organization seeks to support the growth of graduate students in the Chemistry and Biochemistry department by providing professional development opportunities and fostering community and promoting diversity by hosting social events. In addition to maintaining internal connections, the CGSO CHEM Demo Team seeks to connect with the greater Michiana community by hosting chemistry demos for young students and adults alike.

Science Policy Initiative at Notre Dame (SPI@ND)

The Science Policy Initiative at Notre Dame (SPI@ND) seeks to engage all members of the University of Notre Dame, Saint Mary's College, and Holy Cross College campuses in issues at the intersection of Science and Policy. As a member of the Science Policy Network, the group strives to connect all individuals who are passionate about science and are driven to enact science policy change.

To encourage discussion of science policy and professional development of young professionals and trainees, SPI hosts professional development workshops and science policy journal clubs. Recognizing that effective communication of science is a learned skill between scientists and policymakers, young professionals are encouraged and trained to spark science-related dialogue with policymakers at Indiana Science Communication Day (INSciCommDay) at the Indiana Statehouse.

Additionally, SPI works to make science accessible to the public through their monthly Michiana Science Cafes every third Tuesday of each month. Hosted in a casual setting, the Cafes serve to encourage non-science individuals to engage in science-related discussions with scientists.

LASER (Notre Dame Graduate Student Leadership Program)

Founded to foster leadership skills among graduate students, the LASER program offers a series of workshops and networking opportunities throughout the academic year. This program emphasizes the development of essential leadership qualities, such as communication, collaboration, and problem-solving. During the program, participants engage in hands-on projects meant to foster community engagement. LASER provides a platform for students to refine their leadership abilities and connect with peers across disciplines, preparing them for roles in both academia and industry.

Biophysical Society Student Chapter at Notre Dame

Aiming to foster a vibrant community of students passionate about biophysics and related interdisciplinary fields, the Biophysical Society Student Chapter at Notre Dame promotes education, collaboration, and innovation through workshops, seminars, and networking events. We provide a platform for students to engage with faculty, industry professionals, and peers, facilitating discussions on the latest research and techniques in biophysics.

Current & Recent Collaborators