User:Remig/plico
The Plico Suite of Jmol Application Scripts for Modeling Protein Folding
Plico is a suite of Jmol scripts for the visual manipulation by mouse actions of polypeptides (and polynucleotides) in a single-strand or multi-strand environment, accessed as Jmol application macros. It is designed to support modeling the de novo protein folding approach where folding is envisioned to occur as the polypeptide emerges from the ribosome as water and side-chain oxygens (predominantly) disrupt the h-bonds of the alpha helix. The following scripts are implemented or envisioned:
Generate Polypeptide - allows the user to enter a sequence string and have a corresponding alpha helix polypeptide created. The script ribozome.spt and its linking macro can be found here Recycling Corner/Alpha Helix Generator.
Generate Polynucleotide - allows the user to enter a sequence string and have a corresponding single-stranded or double-stranded RNA or DNA polynucleotide created. The script polymeraze.spt and its linkng macro can be found here Recycling_Corner/DNA_Generator.
Tug - allows the user to pull or push by mouse actions to move or rotate one part of a polypeptide against the rest by rotation on its psi and phi bonds with collision detection and restriction. The script tug.spt and its linking macro can be found here User:Remig/plico/tug and its manual found here User:Remig/plico/tugManual.
Tow - allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with collision detection and restriction. The script is currently under development.
Record - allows the user to enter the name of a file to which all Plico commands will be written. The file may be played back to reproduce the users actions. Implemented as just a macro here User:Remig/plico/record.
Freeze - allows the user to mark a section of a polypeptide chain to not have its psi and/or phi bonds rotated by Tug. The script is currently under development.
ToAlpha - allows the user to mark a section of a polypeptide chain to fold towards an alpha helix configuration. The script is currently under development.
ToBeta - allows the user to mark a section of a polypeptide chain to unfold towards a beta strand configuration and possibly form a beta sheet with another strand. The script is currently under development.
Turn - allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click. The script is currently under development.
Hydrate - adds water molecules at appropriate places. The script is currently under development.
Melt - applies side chain rules to unfreeze sections of an alpha helix. The script is currently under development.
FoldRNA - matches complementary internal sections of a single stranded polynucleotide and produces a folded RNA product. The script is currently under development.
CisTrans - toggles prolines between the cis and trans configuration of the omega bond with a mouse click. The script is currently under development.
Remap - Renumbers and re-identifies residues in polypeptide chains. The script remap.spt and its linking macro can be found here User:Remig/plico/remap.
Modify - generates the common polypeptide and polynucleotide modifications: methylation of purines and pyrimidines, hydroxylation of proline, phosphorylation of serine, etc. The script is currently under development.
and more as I think of them...
