PLOP Acknowledgments


The work of MPJ on this code while at Columbia University was funded by the National Science Foundation (Postdoctoral Fellowship in Biological Informatics).


Xin Li (Columbia University) wrote much of the helix prediction code and some of the protonation-state prediction code.  Victor Guallar (Washington U. School of Medicine) contributed an MD code for the academic version of PLOP.  Kai Zhu recently upgraded the routines for calculating RMSDs, using a new dynamic programming algorithm.  Chaok Seok (from Ken Dill's lab at UCSF) and Vageli Coutsias (UNM) have integrated their analytical loop closure algorithm into the academic version of PLOP.   Kai Zhu has improved the minimization algorithms, and David Lev Pincus has improved the loop prediction algorithm (both at Columbia). 


Thanks to Cao, Linda Zhang, and especially Tyler Day at Schrödinger; Zhiyun Yu at Columbia; Chaya Rapp at Yeshiva; CK, Katarzyna, Eli, Ben, Jerome, Ilya, and Sergio from my group; and the Levy group at Rutgers for helping to trouble-shoot the code. 


A few bits of code have been taken from Impact.  The current version uses a few Numerical Recipes routines; these will be replaced in future versions.  Truncated Newton minimizer modified from TNPACK (Tamar Schlick and co-workers).  Helix axis algorithms taken from J. A. Christopher, R. Swanson, and T. O. Baldwin, "Algorithms for finding the axis of a helix:  fast rotational and parameteric least-squares methods", Computers and Chemistry, Vol 20 (1996).  K-means clustering algorithm taken from Appl. Statist. (1979) vol.28, no.1 [Algorithm #136].