POSE (Protein Optimization Steering Environment) is a graphical, interactive environment for the design, modeling, and optimization of protein structures. POSE is a successor of ProteinShop [1,2], a program that facilitates the solution of the protein prediction problem through a combination of interactive features and visualization capabilities. Like ProteinShop, POSE allows users to manipulate protein structures with pinpoint control guided by their biological and experimental instinct. On the other hand, POSE's extended capabilities support other applications like molecular docking. POSE was designed to improve and expand the interactive computing graphics capabilities of ProteinShop. POSE was motivated by our conviction that only such level of interaction will help scientists learn about the complex biological
systems they try to simulate and help them find solutions. Among its main features we would like to highlight: 1) automatic creation of 3-D structures from sequence, 2) manual alignment of beta strands to form beta-sheets, 3) easy coupling with user-provided energy and scoring functions, 4) real-time hydrogen-bond and atom-collision detection, and 5) local minimizations.

About the group


  • Silvia N. Crivelli (Scientist, LBNL/QB3)

Postdoctoral Associates

  • James T. Lu (Senior Research Programmer, QB3)
  • Jinhui Ding (Biologist, QB3)