Computational Structural Biology - Karaca Lab's repositories
gmx_performance_on_HPC
Gromacs performance benchmarking on different HPC platforms
RBD-ACE2-MutBench
Benchmarking the structure-based mutation predictors on ace2-rbd binding data set
Paralog_SDP
Predicting the Specificity-Determining Positions of Paralogous Complexes
AFanalysis
Quick analysis for AlphaFold models
NucDNADynamics
Nucleosomal DNA Dynamics
CASP15_Assembly
Data and analysis scripts of the CASP15 assembly category
DNMT3AB_specificity
an interaction dynamics framework (IDF) applied on DNMT3A/B systems
eif2g-eif2bg-ints
The modeling of eif2g-eif2bg interactions
gmx_corr
gmx_corr converts the covariance matrix which is produced by GROMACS covar to cross correlation matrix and creates a heat map figure.
haddocking.github.io
Webpage of the Bonvinlab @ Utrecht University and HADDOCK software
KDM6A-interacting-models
Contains the structural models of KDM6A, TLE1, HES1, RUNX1-2, HHEX interactions
prot-on_web
This repo contains all necessary codes for deploying the PROT-ON web-server on your local.
RecursiveRMScheck
It calculates the pairwise RMSD values of available pdb files in the folder recursively.
RNN-MD
It is a repo to predict future protein-protein interaction dynamics
traj-to-pdb
This repo creates MD Ensemble pdb from traj and topo files