Roberto Alejandro Calzadilla's starred repositories
proteinshake
Protein structure datasets for machine learning.
carbfix.dat
The carbfix.dat thermodynamic database for PHREEQC
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
POPC_frames_archive
This archive provides the various python scripts required to perform the analyses shown in the paper "Characterizing the dynamic landscape of a bio-membrane with experiment and simulation", by A.A. Smith, A. Vogel, O. Enberg, P. Hildebrand, D. Huster
oRiboT-Fitness-Landscape
Code to map the in vivo fitness landscape of a tethered ribosome
Data-and-Analysis-for-PLCD-Mixtures
Data and Analysis code used in the following paper: "Phase Separation of Protein Mixtures is Driven by the Interplay of Homotypic and Heterotypic Interactions"
CollepardoLab_Chromatin_Model
Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".
public_binding_free_energy_benchmark
The public versio
metabolism_synthesis
Exploration of stream metabolism across > 200 sites
adaptive-simulated-annealing
Adaptive Simulated Annealing (ASA) is a C-language code developed to statistically find the best global fit of a nonlinear constrained non-convex cost-function over a D-dimensional space.
LongReadBenchmark
Benchmarking long-read RNA-seq analysis tools
air-metagenomics
Analysis Pipeline for Minor and Ramuta et al. 2023: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings
imod-python
🐍🧰 Make massive MODFLOW models
gempy
GemPy is an open-source, Python-based 3-D structural geological modeling software, which allows the implicit (i.e. automatic) creation of complex geological models from interface and orientation data. It also offers support for stochastic modeling to address parameter and model uncertainties.