CSB-KaracaLab

prot-on

This repo contains the collection of codes to find designer interfacial mutations

BINDKIN

A structural benchmark to measure point mutations’ impact on kinase-ligand interactions

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

interaction-analysis

Paralog_SDP

Predicting the Specificity-Determining Positions of Paralogous Complexes

AFanalysis

Quick analysis for AlphaFold models

Bulasiciligi-Arttiran-Koronavirus-SARS-CoV-2-Mutasyonlarinin-Tahmini

CSB-WS

This page is prepared to model the complex of phage G3P and E. Coli TolA

NucDNADynamics

Nucleosomal DNA Dynamics

Sox-PTF

CASP15_Assembly

Data and analysis scripts of the CASP15 assembly category

CHEM101.6

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

RecursiveRMScheck

It calculates the pairwise RMSD values of available pdb files in the folder recursively.