Apr 29, 2008
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Source code
VMD Plugin to download and view frames of trajectories
Apr 17, 2008
4 KB
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Source code
Python script to download Trajectory frames
Includes scripts for accessing our archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided.
The villin trajectory archive
The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8.
Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into "frames," also known as a generation. Each "frame" contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1.
For detailed documentation on accessing the archive please see the Wiki (accessible through the left menu).
We also provide the ten starting structures (nine non-folded and the native structure) in the download packages below, (named Project 3037 and 10 packages named Project 3036 RUNx, with x going from 0 to 8, corresponding to the above mentioned "runs" (RUN0-RUN8);
Accessing the Archive
Scripts and VMD plug-in for accessing the archive of villin trajectories. Please see the Wiki for documentation for accessing the archive and the README file (under Documentation links) for using the VMD plug-in.
Release 1.0
Apr 16, 2008
This release contains a python script and a VMD plug-in for viewing and analyzing the trajectories in this project.
Native Structure: Project 3037
This is the native structure, PDB code: 2F4K.
It was used both as the starting point of native state simulations at 300K and by simulations at 373 K (10 ns each using 1 fs time steps) to generate the following nine denatured structures. Additional information below in the Release Notes.
Native structure
May 02, 2008
Download Links
Apr 27, 2009
98 KB
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Data/images/video
PDB file, modified for Amber-96 force field conventions, with water removed, suitable for input to Gromacs with Amber-96.
Apr 27, 2009
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Data/images/video
Link to pdb entry 2F4K, native structure, used as starting point for other conformations in this project.
Project 3036 RUN0
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 0
Apr 10, 2008
Structure 0 shows the presence of Helix 1 and within threshold distances between F6-F10 and F10-F17. Additional information on structural characteristics below in the Notes
Download Links
Apr 15, 2009
44 KB
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Data/images/video
Starting Structure 0 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007) View
Project 3036 RUN1
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 1
Apr 10, 2008
Structure 1 shows the presence of Helix 1 and within threshold distance between F6-F10. Additional information on structural characteristics below in the Notes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 1 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816 (2007) View
Project 3036 RUN2
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 2
Apr 10, 2008
Structure 2 shows a within threshold distances between F10-F17. Additional information on structural characteristics below in theNotes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 2 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN3
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 3
Apr 10, 2008
Structure 2 shows a within threshold distances between F6-F10. Additional information on structural characteristics below in theNotes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 3 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN4
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 4
Apr 10, 2008
One of the two starting structures (4 and 7) that folded much faster than the others. Structure 4 shows the presence of Helix 1 and within threshold distances between F6-F17 and F10-F17.Notes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 4 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN5
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 5
Apr 10, 2008
This starting structure had none of the structural characteristics. Additional information on structural characteristics below in theNotes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 5 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN6
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 6
Apr 10, 2008
This structure had none of the structural characteristicsNotes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 6 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN7
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 7
Apr 10, 2008
One of the two starting structures (4 and 7) that folded much faster than the others. Structure 7 shows the presence of Helix 1 and within threshold distances between F6-F10 and F6-F17. Additional information on structural characteristics below in the Notes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 7 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2007)
Project 3036 RUN8 & RUN9
A great deal of the native structure was lost in these initial structures, but a surprising degree of native-like structure remained. The structural elements considered were the simultaneous presence of the three helices and the six contacts between the three Phe residues, F6, F10 and F17.
Starting Structure 8
Apr 14, 2008
Structure 8 has within threshold distances between all three Phe, F6-F10, F6-F17, F10-F17. Additional information on structural characteristics below in the Notes
Download Links
Apr 15, 2009
44 KB
Any
Data/images/video
Starting Structure 8 in PDB format, compatible with Amber-96 nomenclature.
PLEASE CITE THESE PAPERS
Ensign DL, Kasson PM, Pande VS. "Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece" J. Mol. Biol. 374 (3): 806-816. (2008)