Science Score: 65.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 10 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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✓Institutional organization owner
Organization moldyn has institutional domain (www.moldyn.uni-freiburg.de) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Repository
DESRES trajectory of wild type HP-35 at 360K
Basic Info
- Host: GitHub
- Owner: moldyn
- License: other
- Default Branch: main
- Size: 37.1 KB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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
hp35.dihs: backbone dihedral angels given [degrees]hp35.dihs.shifted: maximum-gap shifted backbone dihedral angels [rad]hp35.crystaldists: the atom distances of all contacts occurring in the crystal structure 2f4k [nm]hp35.mindists: all minimal distances occurring more frequently than 30% [nm]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
$$ \phi2~\psi2~\phi3~\psi3~\ldots~\phi{33} ~\psi{33} ~\phi{34} ~\psi{34} $$
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 ```
Owner
- Name: Biomolecular Dynamics
- Login: moldyn
- Kind: organization
- Location: Freiburg
- Website: http://www.moldyn.uni-freiburg.de/index.html
- Twitter: MolDynFR
- Repositories: 7
- Profile: https://github.com/moldyn
Group of Prof. Dr. G. Stock, University of Freiburg
Citation (CITATION.cff)
cff-version: 1.2.0
title: HP35-DESRES
message: >-
If you use this dataset, please cite it using the metadata
from this file.
type: dataset
authors:
- given-names: Stefano
family-names: Piana
email: Stefano.Piana-Agostinetti@DEShawResearch.com
affiliation: 'D. E. Shaw Research, New York, NY 10036'
- email: Kresten.Lindorff-Larsen@DEShawResearch.com
given-names: Kresten
family-names: Lindorff-Larsen
affiliation: 'D. E. Shaw Research, New York, NY 10036'
- given-names: David E.
family-names: Shaw
email: David.Shaw@DEShawResearch.com
affiliation: >-
Center for Computational Biology and Bioinformatics,
Columbia University, New York, NY 10032
identifiers:
- type: doi
value: 10.1073/pnas.1201811109
preferred-citation:
type: article
title: "Protein folding kinetics and thermodynamics from atomistic simulation"
authors:
- given-names: Stefano
family-names: Piana
- given-names: Kresten
family-names: Lindorff-Larsen
- given-names: David E.
family-names: Shaw
doi: "10.1073/pnas.1201811109"
journal: "Proc. Natl. Acad. Sci. USA"
month: 10
start: 17845
end: 17850
issue: 44
volume: 109
year: 2012
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