Tom Ferrin, PhD

Phone: +1 415 476-2299
600 16th St, Rm N472E
UCSF Box 2240
San Francisco, CA 94158
United States


What I do

My lab develops software tool for visualizing and analyzing molecular structures at scales ranging from the atomic to the supramolecular.

Departmental research area

My research expertise

biological and medical informatics, biocomputing, visualization, informatics, pharmaceutical chemistry, bioengineering and therapeutic sciences

Professional background


My research focuses on developing cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualization and analyses of molecular structures and related non-structural biological information. Our tools are applied daily to diverse types of biomolecular data, including atomic-resolution coordinates, 3D cryo-EM and X-ray density maps, light microscopy data sets, and protein and nucleic acid sequences, annotations, and networks. Our primary research efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure relationships, and network representations of protein similarity, binding interactions, and biological pathways. These areas are critical for addressing important and highly relevant biomedical problems such as identifying the molecular bases of disease, annotating proteins of unknown function, identifying targets for drug development, designing new drugs, and engineering proteins with new functions. For many years we have been disseminating well-documented and robust software tools via our web site so that scientists world-wide can advance their own research programs effectively. Our current software development efforts are focused on ChimeraX, our next-generation desktop app for the interactive visualization and analysis of molecular structures and related data.

Research keywords

  • Imaging, Three-Dimensional
  • Protein Databases
  • software
  • Molecular Conformation
  • Molecular Models
  • Chlamydia trachomatis
  • Sequence Alignment
  • Protein Sequence Analysis
  • computational biology
  • computer graphics
  • Organic Cation Transport Proteins
  • proteins
  • User-Computer Interface
  • Protein Conformation
  • Molecular Sequence Annotation