SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

TLDR

Comparative protein modeling is increasingly used to aid rational design of mutagenesis experiments, but its adoption has been limited by costly hardware and software. We developed an environment combining SWISS‑MODEL, an automated modeling server, and SWISS‑PdbViewer, a sequence‑to‑structure workbench, to overcome these limitations. SWISS‑PdbViewer serves as a client for SWISS‑MODEL and offers extensive structure analysis and display tools, while the SWISS‑MODEL Repository hosts over 3,500 automatically generated protein models. By freely providing these tools, we aim to broaden the use of protein structures and models in experimental design.

Abstract

Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.