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Computational Biochemistry

What is Computational Biochemistry?

Computational Biochemistry research develops and utilizes mathematical models, computer simulations, and statistical tools to address big questions in biology. This field is especially important in the 21st century as the volume and quality of large datasets has advanced more rapidly than our ability to analyze them.

What is the impact of our research in Computational Biochemistry?

  • Pathogenic drug resistance can be predicted by computational algorithms, allowing scientists to avoid developing compounds that are more likely to lead to resistance. Find out more here.
  • New drugs for various diseases can be designed by studying computer models of protein-compound interactions. Find out more here.
  • The way genome sequence impacts human health is being elucidated in part by scientists in our department developing new analytical pipelines to interpret large datasets. Find out more here.

 

Who's studying Computational Biochemistry?

  • Daniel Bolon

    Daniel Bolon, PhD

    Professor of Biochemistry & Molecular Biotechnology

    Type: Primary

    Areas of Research: Biochemical Mechanisms, Cellular Biochemistry, Computational Biochemistry

    Category: CLIM/Ldb cofactors,disease prevention

    Research Interest: The Bolon Lab investigates relationships between protein sequence, structure and function.

    Broader Impact: COVID-19, cancer, HIV

    Office Location: LRB 922
    Lab Location: LRB 960 E-D
    Phone: 508-856-3588

    Lab Page

  • Julia Flynn

    Julia Flynn, PhD

    Assistant Professor of Biochemistry & Molecular Biotechnology; Member of the Bolon Lab.

    Type: Primary

    Areas of Research: Biochemical Mechanisms, Cellular Biochemistry, Computational Biochemistry

    Research Interest: Dr. Flynn investigates how changes in DNA sequence impact protein function.

    Key Words: drug resistance, protein adaptation, protein folding, evolution, mutagenesis, deep mutational scanning

    Research Tools: S. cerevisiae (yeast)

    Broader Impact: cancer, SARS-CoV2

    she/her/hers
    Lab Location: LRB 960 D
    Phone: 508-856-4418

  • Brian Kelch

    Brian Kelch, PhD

    Associate Professor of Biochemistry & Molecular Biotechnology

    Type: Primary

    Areas of Research: Biochemical Mechanisms, Biophysics & Macromolecular Structures, Computational Biochemistry

    Research Interest: The Kelch Lab utilizes structural biology and biochemistry to reveal the workings of large macromolecular complexes, with a special focus on those involved in DNA replication/repair and virus assembly. 

    Research Tools: E. coli (bacteria), S. cerevisiae (yeast), T. thermophilus (bacteria), H. sapiens (human)

    Broader Impact: cancer, PARD, infectious disease

    he/him/his
    Office Location: LRB 923
    Lab Location: LRB 970 H-G
    Phone: 508-856-8322

    Lab Page

     

  • Nese Kurt Yilmaz

    Nese Kurt Yilmaz, PhD

    Associate Professor of Biochemistry & Molecular Biotechnology

    Type: Primary

    Areas of Research: Biochemical Mechanisms, Biophysics & Macromolecular Structures, Computational Biochemistry

    Research Interest: Biological function, enzyme inhibition and drug resistance.
     

    Key Words:
    protein structure, biomolecular complexes, conformational dynamics, enzyme inhibition

    Research Tools: viral proteases, deaminases, renalase

    Broader Impact: Viral infections (HIV-1, HCV, coronaviruses, influence, dengue), cancer, type I diabetes

    Office Location: LRB 919
    Phone: 508-856-1867

    Lab Page 

  • Francesca Massi

    Francesca Massi, PhD

    Associate Professor of Biochemistry & Molecular Biotechnology

    Type: Primary

    Areas of Research: Biochemical Mechanisms, Biophysics & Macromolecular Structures, Computational Biochemistry, Gene Expression & Epigenetics

    Research Interest: The Massi lab uses their expertise in NMR Spectroscopy to understand the dynamics of protein-RNA interactions.

    Office Location: LRB 925
    Lab Location: LRB 960 B, 970 N
    Phone: 508-856-4501

    Lab Page

  • Oliver J. Rando

    Oliver J. Rando, MD, PhD

    Professor of Biochemistry & Molecular Biotechnology

    Type: Primary

    Areas of Research: Cellular Biochemistry, Computational Biochemistry, Gene Expression & Epigenetics

    Research Interest: The Rando Lab studies the role of epigenetic inheritance in programming health and disease.

    Key Words: epigenetics, chromatin, small non-coding RNA, embryology, spermatogenesis

    Research Tools: S. cerevisiae (yeast), M. musculus (mouse), C. elegans (nematode worm)

    Broader Impact: Paternal environments can affect diabetes, metabolic syndrome, anxiety, schizophrenia and more.

    he/him/his
    Office Location: LRB 906
    Lab Location: LRB 940 A-C &
    LRB 970 X-Y
    Phone: 508-856-8879

    Lab Page

  • Celia Schiffer

    Celia Schiffer, PhD

    Chair & Arthur F. and Helen P. Koskinas Professor of Biochemistry and Molecular Biotechnology, and Director of the Institute for Drug Resistance

    Type: Primary

    Areas of Research: Biophysics & Macromolecular Structures, Chemical Biology, Computational Biochemistry

    Research Interest: The Schiffer Lab studies the molecular basis for drug resistance and has developed a new paradigm for avoiding drug resistance when targeting enzymes in structure-based drug design.

    Research Tools:
     protein crystallography, CryoEM/CryoET, molecular dynamics simulations, homology modeling, enzymatic assays and medicinal chemistry,

    Broader Impact: RNA Viruses (HIV, HTLV, Influenza, Coronaviruses, Enteroviruses, Flaviviruses) and Cancer

    Office Location: LRB 928
    Lab Location: LRB 840 D; 860 C; 960 E; 970 C, D, L, M
    Phone: 508-856-8008
      
    Lab Page

  • Chen Xu

    Chen Xu, PhD

    Professor of Biochemistry & Molecular Biotechnology; Director of the Cryo-Electron Microscopy Core Facility

    Type: Primary

    Areas of Research: Biophysics & Macromolecular Structures, Computational Biochemistry

    Research Interest: The Xu lab is constantly researching ways to increase accessibility of Cryo-EM techniques.

    Key Words: Cryo-electron Microscopy, Structural Biology

    Research Tools: Cryo-Electron Microscopy

    Office Location: LRB 902 & 
    SA-106
    Lab Location: SA-106
    Phone: 774-455-4050
     
    Lab Page

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