About

Christopher Brooks, MD, is an allergy and immunology physician and an Assistant Professor at The Ohio State University Wexner Medical Center. He specializes in treating a variety of conditions related to allergy and immunology, including seasonal allergies, food-related symptoms, recurrent infections, and complex immunological disorders. Dr. Brooks is committed to providing inclusive, individualized, and compassionate care, ensuring that each patient understands all their options before proceeding with a treatment plan. He emphasizes the use of innovative, evidence-based treatments, leveraging advancements in genetic testing and biologic therapies. His academic and research efforts focus on immunotherapy, including intralymphatic immunotherapy, and improving processes to eliminate unnecessary drug allergies from patients' allergy lists. Dr. Brooks is actively involved in research and education, mentoring medical students and participating in community service through volunteer work with the Columbus Free Clinic and the Medical Reserve Corps. He is dedicated to community service and advocacy for improved access to quality healthcare, working with various organizations and legislators to address healthcare disparities. His background includes a fellowship in Allergy & Immunology at Ohio State University Wexner Medical Center, and he holds certifications from the American Board of Allergy & Immunology and the American Board of Pediatrics.

Research topics

• Computer Science
• Biology
• Combinatorics
• Artificial Intelligence
• Mathematics
• Chemistry
• Geology
• Bioinformatics
• Biological system
• Biochemical engineering
• Computational biology
• Materials science
• Computational chemistry
• Telecommunications
• Database
• Algorithm
• Genetics
• Statistical physics
• Nanotechnology
• Engineering
• Physics
• Virology

Selected publications

• Core Flipping in Lead Optimization: Rank Ordering using Multisite λ Dynamics

  2024

  • Computer Science
  • Statistical physics
  • Computer Science

  In structure-based drug discovery, reliable structural models of ligands bound to their target receptor are critical for establishing the structure activity relationship of congeneric series. In such a series, substitutions on a common scaffold core might lead to different binding modes, ranging from slight changes of orientations to flipping or inversion of the core structure. Moreover, molecular docking might lead to alternative orientations within the top ranked poses without being able to discriminate which is the most likely. To determine the relative binding affinities between two alternative ligand poses, we propose a methodology based on relative binding free energy calculations using the multisite λ dynamics method. We use a dual-topology approach with distance restraining schemes. We introduced a novel strategy using one-step perturbation to calculate the contributions of the applied restraints. While using FEP/MBAR instead for that purpose led to smaller uncertainties it suffered from convergence issues. We test the validity and predictive power of our approach using two pharmaceutically relevant targets and eight compounds from experimentally characterized congeneric series. For each target, our approach correctly ranks the known X-ray poses to be more favorable than alternative flipped poses. The proposed methodology can be easily extended to rank more than two poses in a single simulation and should also be applicable for the prediction of conformational binding cliffs, ranking fragments, core hopping cases and evaluating different scaffold binding to a common target.

  PublisherOA PDFDOI

• Core Flipping in Lead Optimization: Rank Ordering using Multisite λ Dynamics

  2024 · 1 citations

  • Computer Science
  • Artificial Intelligence
  • Computer Science

  In structure-based drug discovery, reliable structural models of ligands bound to their target receptor are critical for establishing the structure activity relationship of congeneric series. In such a series, substitutions on a common scaffold core might lead to different binding modes, ranging from slight changes of orientations to flipping or inversion of the core structure. Moreover, molecular docking might lead to alternative orientations within the top ranked poses without being able to discriminate which is the most likely. To determine the relative binding affinities between two alternative ligand poses, we propose a methodology based on relative binding free energy calculations using the multisite λ dynamics method. We use a dual-topology approach with distance restraining schemes. We introduced a novel strategy using one-step perturbation to calculate the contributions of the applied restraints. While using FEP/MBAR instead for that purpose led to smaller uncertainties it suffered from convergence issues. We test the validity and predictive power of our approach using two pharmaceutically relevant targets and eight compounds from experimentally characterized congeneric series. For each target, our approach correctly ranks the known X-ray poses to be more favorable than alternative flipped poses. The proposed methodology can be easily extended to rank more than two poses in a single simulation and should also be applicable for the prediction of conformational binding cliffs, ranking fragments, core hopping cases and evaluating different scaffold binding to a common target.

  PublisherOA PDFDOI

• VIPERdb v3.0: a structure-based data analytics platform for viral capsids

  Nucleic Acids Research · 2020 · 77 citations

  • Computer Science
  • Biology
  • Computational biology

  VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called 'Virus World database' (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.

  PublisherDOI

• Enjoying sad music: A test of the prolactin theory

  Musicae Scientiae · 2019-12-25 · 41 citations

  article

  Philosophers have long wrestled with the apparent paradox of the enjoyment of negative emotional portrayals in the arts. An example of this apparent paradox is the enjoyment among some listeners of nominally sad music. An experiment is reported in which 39 participants listened to sad and happy music while serum prolactin (PRL) concentrations were measured. The purpose of the experiment was to test an a priori theory, proposed by Huron, that liking sad music is mediated by elevated PRL levels. Contrary to the theory, sad music did not result in a significant increase in PRL; nor was the pleasure of listening to sad music associated with increased PRL. Nominally happy music did result in a decrease of PRL, especially for those participants who most prefer happy music over sad music. The effect was greatest for those who score high on a measure of loneliness. Consistent with other studies, the degree of liking sad music over happy music was found to correlate with trait openness to experience, although this effect was not echoed in PRL levels. Post-hoc analyses indicate that PRL decreases were most marked for male listeners and those who score high on a loneliness measure. In general, the results are not consistent with the theory proposed by Huron.

  PublisherDOI

• Structural Basis for Selectivity in Flavin-Dependent Monooxygenase-Catalyzed Oxidative Dearomatization

  ChemRxiv · 2018-11-06

  preprintOpen access

  Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by the first crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data.

  PublisherOA PDFDOI

• Protein Phosphorylation of Prolactin Target Tissue: Mammary Gland

  2018-01-10

  book-chapter1st authorCorresponding

  This chapter reviews protein phosphorylation in one prolactin target tissue, the mammary gland. In relating the molecular actions of prolactin to protein phosphorylations one will realize that few, if any, prolactin-regulated protein kinases or phosphatases have yet been documented. The phosphorylation of proteins occurs as an enzymatically mediated posttranslational modification. Phosphate is covalently attached to the side group of serine, threonine, or tyrosine. Phosphorylation of proteins may be permanent, such as caseins, or may be transient, as the phosphorylation and dephosphorylation reactions of substrate enzymes such as glycogen synthase. Protein phosphorylation has been successfully studied in several different experimental systems. These include in vivo studies, whole cell homogenates or subcellular organelles, and isolated protein systems. Protein kinases have been classified by a number of properties, including their substrate specificities, biochemical characteristics, or regulatory mechanisms. Fatty acid synthesis occurs in the cytosolic fatty acid synthase complex.

  PublisherDOI

• Tuning RNA folding and function through rational design of junction topology

  Nucleic Acids Research · 2017-07-05 · 11 citations

  articleOpen accessCorresponding

  Structured RNAs such as ribozymes must fold into specific 3D structures to carry out their biological functions. While it is well-known that architectural features such as flexible junctions between helices help guide RNA tertiary folding, the mechanisms through which junctions influence folding remain poorly understood. We combine computational modeling with single molecule Förster resonance energy transfer (smFRET) and catalytic activity measurements to investigate the influence of junction design on the folding and function of the hairpin ribozyme. Coarse-grained simulations of a wide range of junction topologies indicate that differences in sterics and connectivity, independent of stacking, significantly affect tertiary folding and appear to largely explain previously observed variations in hairpin ribozyme stability. We further use our simulations to identify stabilizing modifications of non-optimal junction topologies, and experimentally validate that a three-way junction variant of the hairpin ribozyme can be stabilized by specific insertion of a short single-stranded linker. Combined, our multi-disciplinary study further reinforces that junction sterics and connectivity are important determinants of RNA folding, and demonstrates the potential of coarse-grained simulations as a tool for rationally tuning and optimizing RNA folding and function.

  PublisherOA PDFDOI

• Editorial

  Protein Science · 2015-12-28

  editorialOpen accessSenior authorCorresponding

  Peer Reviewed

  PublisherOA PDFDOI

• Enhanced Sampling Assisted Flexible Fitting of Atomic Structures into Electron Microscopy Maps

  Biophysical Journal · 2013-01-01

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Molecular Simulations of pH-Dependant Maturation-Associated Structural Changes in Bacteriophage HK97

  Biophysical Journal · 2013-01-01

  articleOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• NIH Grant R01DK072275

  NIH · $1.0M · 2010

• Multiscale Modeling and Enhanced Sampling of Protein-Protein Recognition

  NSF · $1.2M · 2015–2021

• NIH Grant K04DK001989

  NIH · $324k · 1996

• NIH Grant R01HD021130

  NIH · $271k · 1991

• NIH Grant R01DK056117

  NIH · $1.0M · 2004

Frequent coauthors

• Eugene R. DeSombre

  University of Chicago

  7 shared

• John R. Latendresse

  7 shared

• Lawrence J. Berliner

  University of Denver

  7 shared

• Vijay Reddy

  Scripps Institution of Oceanography

  6 shared

• Elwood V. Jensen

  6 shared

• Dmitry B. Veprintsev

  Paul Scherrer Institute

  6 shared

• Vladimir N. Uversky

  5 shared

• Jeffrey M. Canfield

  5 shared

Labs

• Otolaryngology & Head and Neck Surgery - Allergy & ImmunologyPI

Awards & honors

• Chrysalis Project scholarship from a national allergy organi…
• Commitment to Service Award from The Ohio State University