RCD+ intro

Random Coordinate Descent (RCD) is a versatile loop closure tool to efficiently generate loop ensembles. The algorithm solves the loop closure problem by optimizing randomly selected bonds and updating loop conformations using spinor matrices (geometric algebra). At download section you can get the latest version of RCD. Additionally, an online protein loop prediction server is available at rcd.chaconlab.org.
New 2016 version available! (v1.11)

References


Server and improved method

López-Blanco JR, Canosa-Valls AJ, Li Y, and Chacón P (2016). RCD+: Fast loop modeling server. Nucl. Acids Res. 44 (W1): W395-W400.

Original method

Chys P and Chacón P (2013). Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure. J. Chem. Theory Comput. 9:1821-1829.