Predicting allosteric communication in myosin via a conserved residue pathway
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AlloPathFinder
The application Allopathfinder facilitates the computation of the "best paths" between two locations in a protein 'structure'. Please download the AlloPathFinderUsersGuide.pdf first to learn about the application. For instructions on how to reproduce the paths for the structures in Figure 3 of our publication please download the file RunningAlloPathFinder.txt under 'Documentation Links' below.
Release 1.1
May 07, 2007

Notes  

Download Package

Download Links

AlloPathFinder Executable for windows

AlloPathFinder1.1.exe
Jun 18, 2009
7 MB
Windows
Application/binary
Executable for windows platform.

ActiveState Perl (needed for AlloPathFinder)

LinkToActiveStatePerlDownloads (URL)
Jun 18, 2009
0
Windows
Application/binary
You will need ActiveState Perl V.5.8.x to run AlloPathFinder (see the Users Guide for additional information)

PyMol (not required but recommended for AlloPathFi

PyMol Home Page (URL)
Jun 18, 2009
0
Windows
Application/binary
Link to PyMol Home Page, not required for AlloPathFinder, but recommended.

Documentation Links

Download first

AlloPathFinderUsersGuide.pdf
Jul 10, 2008
User Guide for AlloPathFinder, updated July 2008 to include example input values and Vista installation instructions

RunningAlloPathFinder.txt
Nov 11, 2008
Instructions for running AllopathFinder on the 14 structures reported in Figure 3 of our paper.

Sample input files

MyosinMSA_158.aln
May 10, 2007
Comprehensive multiple sequence alignment of 158 myosin sequences, suitable as input to AlloPathFinder1.1.exe

Myosin_1VOM.pdb
May 10, 2007
PDB structure for 1VOM, suitable as input to AlloPathFinder1.1.exe

PLEASE CITE THESE PAPERS

Tang S, Liao JC, Dunn A, Spudich JA, Altman RB, Schmidt J. "Predicting allosteric communication in myosin via a pathway of conserved residues." Journal of Molecular Biology, 373, 1361–1373. (2007) View

Previous Releases


v.1

Mar 14, 2007

First Release of AlloPathFinder. AlloPath.exe runs on Windows platform only  

Download Package

Download Links

AlloPathFinder executables

AlloPathFinder.exe
Mar 24, 2007
7 MB
Windows
Application/binary
Executable for windows platform

AlloPathFinder_05_07_07.exe
May 08, 2007
7 MB
Windows
Application/binary

AlloPathFinder_04_28_07.exe
Apr 29, 2007
7 MB
Windows
Application/binary

Documentation Links

AlloPathFinderUsersGuide.pdf
Mar 23, 2007
Users Guide -- please download this first


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AlloPathFinderExampleData
This package contains additional PDB files that can be used as examples for running the AlloPathFinder software. Consult RunningAlloPathFinder.txt in the AlloPathFinder Package on how to use these in conjunction with the MyosinMSA_158.aln multiple alignment file to reproduce the paths reported in Figure 3 of JMB 373,1361–1373.
data v.1
Mar 14, 2007

  

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Myosin Prestroke Structures

1VOM.pdb
Mar 10, 2007
553 KB
Any
Data/images/video
1VOM PDB File ((Dictyostelium Myosin II -- Preprocessed)

1QVI.pdb
Mar 12, 2007
758 KB
Any
Data/images/video
1QVI PDB File (Scallop Myosin II -- Preprocessed)

1BR2.pdb
Nov 08, 2008
2 MB
Any
Data/images/video
1BR2 PDB file (Chicken Myosin II)

1LKX.pdb
Nov 08, 2008
1 MB
Any
Data/images/video
1LKX.pdb (Dictyostelium Myosin I)

1W9J.pdb
Nov 08, 2008
550 KB
Any
Data/images/video
1W9J.pdb (Dictyostelium Myosin II)

1YV3.pdb
Nov 08, 2008
555 KB
Any
Data/images/video
1YV3.pdb (Dictyostelium Myosin II)

1FMV.pdb
Nov 09, 2008
552 KB
Any
Data/images/video
1FMV PDB file (Dictyostelium Myosin II)

1FMW.pdb
Nov 09, 2008
549 KB
Any
Data/images/video
1FMW.pdb (Dictyostelium Myosin II)

1KK7.pdb
Nov 09, 2008
706 KB
Any
Data/images/video
1KK7 PDB File (Scallop Myosin II -- Preprocessed)

Myosin Rigor structures

1MMA.pdb
Nov 09, 2008
492 KB
Any
Data/images/video
1MMA (Dictyostelium Myosin II)

1MMD_Dicty_II_mutated.pdb
Nov 09, 2008
530 KB
Any
Data/images/video
1MMD (Dictyostelium Myosin II)

1W7J.pdb
Nov 09, 2008
648 KB
Any
Data/images/video
1W7J.pdb (Chicken Myosin V)

1W9I.pdb
Nov 09, 2008
579 KB
Any
Data/images/video
1W9I.pdb (Dictyostelium Myosin II)

Myosin Post-rigor Structures

2AKA.pdb
Nov 10, 2008
788 KB
Any
Data/images/video
2AKA.pdb (Dictyostelium Myosin II)

1OE9.pdb
Nov 10, 2008
624 KB
Any
Data/images/video
1OE9.pdb (Chicken Myosin V)

Figure 3 from JMB, 373, 1361-1373.

Copy_of_Figure3.pdf
Nov 12, 2008
77 KB
Any
Data/images/video
Figure 3 and it's legend from JMB 373, 1361-1373.

FASTA file of Myosin Sequences

23315349.fasta
Mar 09, 2007
246 KB
Any
Data/images/video
Fasta File for MyosinMSA_158.aln

PLEASE CITE THESE PAPERS

Tang S, Liao JC, Dunn A, Spudich JA, Altman RB, Schmidt J. Predicting allosteric communication in myosin via a pathway of conserved residues. Journal of Molecular Biology, 373, 1361–1373 (2007) View


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