Software:Loopy General Description
From Honiglab_public
Introduction:
loopy is a program for protein loop prediction, sequence mutation and addition of a missing protein segment. If the segment to be predicted already exists, loopy will delete the original segment and predict a new one to assemble onto the stems. If the segment to be predicted does not exist, the residue sequence of the missing segment must be provided and loopy will predict a segment with those residues and assemble it onto the two end stems. To make mutations to all of the residues in a protein segment, loopy will treat this as loop prediction as the case where the segment is missing described in the second case above. Segment mutation can also be done using our side-chain prediction program (scap). The difference is that in scap, the backbone is fixed while in loopy the backbone is to be predicted.
The loopy program first builds multiple initial conformations using an ab-initio method. Each of the conformation is then closed using random tweak method. Fast energy minimization in torsional angle space is then performed (paper under preparation) and side-chain is assembled using the scap program. Colony energy is used to sort out the best predictions. For details, please check our loopy paper (submitted).
The loopyMod program is similar to loopy (see description for loopy). There a couple of minor differences in how the loops are energy minimized which may result in loopy and loopyMod giving different results. However, these differences are minor and were done only to improve the speed. loopyMod has the ability to output all loop conformations to a single file in a PDB-NMR style format. This allows the user the option to consider alternate loop conformations instead of relying on loopy’s energy function to select the most favorable conformation. At the request of some users, we have included the "Random Tweak" option for anyone who wants to quickly generate loop backbone conformations. In theory, one could use loopy to generate the loop conformations, however, loopyMod makes generating the ensemble of loop conformations fast since the number of file IO operations is drastically reduced.
LoopBuilder is a fast and accurate protocol, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations (loopyMod), side chain addition, the use of a statistical potential to select a subset of these conformations (Dfire), and, finally, an energy minimization and ranking with an all-atom force field (PLOP). The first two programs (loopyMod and Dfire) can be downloaded from this site. Unfortunately, we cannot distribute PLOP. Instead, users should go to: http://jacobson.compbio.ucsf.edu/plop_manual/plop_overview.htm
loopy is supported by a funding from the National Science Foundation Grant # DBI-9904841.
loopyMod is supported by a funding from the National Science Foundation Grant # MCB-0416708 and
funding from the National Institute of Health Grant # GM30518.
Developed in the Honig Lab
