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.

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 linking macro can be found here.

Tug - is the core of the Plico suite. It 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. It also allows the user to pull or push by mouse actions to move or to rotate an entire chain or chains with auto-rotation to nest one chain against another. The script tug.spt and its linking macro can be found here and its manual found here.

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.

Remap - Renumbers and re-identifies residues in polypeptide chains. The script remap.spt and its linking macro can be found here.

RemapNT - Renumbers and re-identifies residues in polynucleotide chains. The script remapNT.spt and its linking macro can be found here.

Turn - allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click as well as cis/trans rotations on proline omega bonds. The script turn.spt and its linking macro can be found here.

ToAlphaBeta - allows the user to mark a section of a polypeptide chain to fold towards an alpha helix configuration or towards a beta strand configuration. The script toAlphaBeta.spt and its linking macro can be found here and its manual found here.

Modify - generates the common polypeptide and polynucleotide modifications: methylation of purines and pyrimidines, hydroxylation of proline, phosphorylation of serine, etc. The script modify.spt and its linking macro can be found here.

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.

ToBetaSheet - allows the user to mark a section of a polypeptide chain to form a beta sheet with another strand. 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.

and more as I think of them...

Contributors

Remig