HP35-DESRES

Citations

Using any file from this repository, please cite the following article:

S. Piana, K. Lindorff-Larsen, and D. E. Shaw,
Protein folding kinetics and thermodynamics from atomistic simulation,
Proc. Natl. Acad. Sci. USA 109, 17845 (2012)
doi: 10.1073/pnas.1201811109

Provided Data

The time series of three different internal coordinate representations of the Nle/Nle mutant of the villin headpiece (HP35), generated from a 300μs long molecular dynamics simulation (Amber99SB-ILDN) at 360K, are given. Please read the license carefully before use.

DEPENDENCY: git-lfs is needed for large file support

1. hp35.dihs: backbone dihedral angels given [degrees]
2. hp35.dihs.shifted: maximum-gap shifted backbone dihedral angels [rad]
3. hp35.crystaldists: the atom distances of all contacts occurring in the crystal structure 2f4k [nm]
4. hp35.mindists: all minimal distances occurring more frequently than 30% [nm]
5. hp35.mindists2: improved distances definition with all atom pairwise distances occurring more frequently than 30% [nm]

Backbone Dihedral Angles

The time series of all backbone dihedral angles from residue 2 to residue 34 are given in the file hp35.dihs (in degrees !), while in hp35.dihs.shifted the maximal gap shifting method (Sittel et al. 2017) was applied to allow non-periodic treatment of the angles.

The columns correspond to

$$ \phi_2~\psi_2~\phi_3~\psi_3~\ldots~\phi_{33} ~\psi_{33} ~\phi_{34} ~\psi_{34} $$

which can be also found in the file hp35.dihs.names.

Contact Distances

The time series of all minimal distances $d_{ij}$ using the following two different approaches suggested by Nagel et al. 2023. For hp35.mindists the distance between the residues $i$ and $j$ is given by the minimal distance of the heavy atoms $n\in i$, $m\in j$, so

$$ d_{ij}(t) = \min_{n,m} |\mathbf{r}_ {i, n}(t) - \mathbf{r}_ {i, n}(t)| $$

and a contact distance must be below $0.45:\text{nm}$ with probability $P_{ij}\ge 0.3$.

The second definition, used in hp35.mindists2, takes the minimum only over all atomic distances $n$, $m$ which are formed more frequent than $0.3$, so

$$ d_{ij}(t) = \min_{P_{n,m}\ge 0.3} |\mathbf{r}_ {i, n}(t) - \mathbf{r}_ {i,n}(t)|;.$$

The indices corresponding to each column can be found in hp35.mindists.ndx and hp35.mindists2.ndx, respectively.

Using these contact definitions, please cite:

D. Nagel, S. Sartore, and G. Stock,
Selecting Features for Markov Modeling: A Case Study on HP35,
J. Chem. Theory Comput., submitted
doi: 10.48550/ARXIV.2303.03814

Getting-Started

Quick-start to check and unzip all datasets:

git clone https://github.com/moldyn/HP35-DESRES.git
cd HP35-DESRES
# check if corrupt
for data in hp35.*.bz2; do
  bunzip2 -t $data &>/dev/null || echo "file $data corrupt, please download again."
done
# unzip all
for data in hp35.*.bz2; do
  bunzip2 -k $data
done