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 lab develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. Our tools can be applied to diverse types of biomolecular data, including atomic-resolution coordinates, 3D density maps and light microscopy data, and protein and nucleic acid sequences, annotations, and networks. We focus on unmet software needs for basic and applied biomedical research using highly trained and talented staff, with excellent interdisciplinary knowledge and specialized, state-of-the-art expertise in software engineering, computer graphics visualization, and data analysis. Our primary efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure-function 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, identifying targets for drug development, designing drugs, and engineering proteins with new functions.

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