PolyFold

PolyFold is an interactive visual simulator for distance-based protein folding. The goal of PolyFold is to give both researchers and non-experts an intuitive and easy-to-use visual interface which elucidates the process of distance-based protein folding. PolyFold embeds powerful stochastic optimization algorithms with on-demand customizations and interactive manipulations in real-time to fold a protein molecule through the satisfaction of spatial constraints derived from a protein's inter-residue distance matrix.

If you find PolyFold useful, please cite our PLOS ONE paper. A detailed user manual of PolyFold is available here, accompanying the paper as supplementary documentation.

<img src='Assets/gd.gif' width='100%'/> <p align='center'> <em>PolyFold optimizes the CASP target T0864 in real-time via its Batch Gradient Descent feature</em> </p>

Dataset

PolyFold's source code includes with it a set of 20 curated residue-residue interaction map files for various sized protein targets. Each entry in the table below contains a GIF visualization of the interaction map for one of these proteins as it is optimized. Each GIF has a label below it with the protein's name and the number of residues in that protein in parenthesis. All GIFs also link to the raw RR file for download for their respective protein.

<a href="Dataset/1guuA.rr"><img src="Assets/1guuA.gif" width="150" height="150"/></a> | <a href="Dataset/1brfA.rr"><img src="Assets/1brfA.gif" width="150" height="150"/></a> | <a href="Dataset/1aapA.rr"><img src="Assets/1aapA.gif" width="150" height="150"/></a> | <a href="Dataset/1jo8A.rr"><img src="Assets/1jo8A.gif" width="150" height="150"/></a> | <a href="Dataset/1ku3A.rr"><img src="Assets/1ku3A.gif" width="150" height="150"/></a> :-: | :-: | :-: | :-: | :-: 1guuA (50) | 1brfA (53) | 1aapA (56) | 1jo8A (58) | 1ku3A (61) <a href="Dataset/1m8aA.rr"><img src="Assets/1m8aA.gif" width="150" height="150"/></a> | <a href="Dataset/1c9oA.rr"><img src="Assets/1c9oA.gif" width="150" height="150"/></a> | <a href="Dataset/1vfyA.rr"><img src="Assets/1vfyA.gif" width="150" height="150"/></a> | <a href="Dataset/1ctfA.rr"><img src="Assets/1ctfA.gif" width="150" height="150"/></a> | <a href="Dataset/1kw4A.rr"><img src="Assets/1kw4A.gif" width="150" height="150"/></a> 1m8aA (61) | 1c9oA (66) | 1vfyA (67) | 1ctfA (68) | 1kw4A (70) <a href="Dataset/1cc8A.rr"><img src="Assets/1cc8A.gif" width="150" height="150"/></a> | <a href="Dataset/1atzA.rr"><img src="Assets/1atzA.gif" width="150" height="150"/></a> | <a href="Dataset/1tifA.rr"><img src="Assets/1tifA.gif" width="150" height="150"/></a> | <a href="Dataset/1h98A.rr"><img src="Assets/1h98A.gif" width="150" height="150"/></a> | <a href="Dataset/1t8kA.rr"><img src="Assets/1t8kA.gif" width="150" height="150"/></a> 1cc8A (72) | 1atzA (75) | 1tifA (76) | 1h98A (77) | 1t8kA (77) <a href="Dataset/1a3aA.rr"><img src="Assets/1a3aA.gif" width="150" height="150"/></a> | <a href="Dataset/1xdzA.rr"><img src="Assets/1xdzA.gif" width="150" height="150"/></a> | <a href="Dataset/T0864.rr"><img src="Assets/T0864.gif" width="150" height="150"/></a> | <a href="Dataset/T0950.rr"><img src="Assets/T0950.gif" width="150" height="150"/></a> | <a href="Dataset/T0966.rr"><img src="Assets/T0966.gif" width="150" height="150"/></a> 1a3aA (145) | 1xdzA (238) | T0864 (246) | T0950 (342) | T0966 (492)

Installation

The provided manual gives instructions for building PolyFold from source or installing the pre-packaged versions of PolyFold for Mac, Linux, and Windows.