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Computational Structural Biology - Karaca Lab (CSB-KaracaLab)

CSB-KaracaLab

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Company:Izmir Biomedicine and Genome Center

Location:Izmir, Turkey

Home Page:https://www.ibg.edu.tr/research-programs/groups/karaca-lab/

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Computational Structural Biology - Karaca Lab's starred repositories

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

License:GPL-3.0Stargazers:1387Issues:0Issues:0

ai-for-grant-writing

A curated list of resources for using LLMs to develop more competitive grant applications.

Language:PythonLicense:CC-BY-4.0Stargazers:1770Issues:0Issues:0

DNMT3AB_specificity

Language:Jupyter NotebookStargazers:3Issues:0Issues:0

AF2Rank

Language:Jupyter NotebookLicense:MITStargazers:92Issues:0Issues:0

AFanalysis

Quick analysis for AlphaFold models

Language:PythonStargazers:1Issues:0Issues:0

AFanalysis

Quick analysis for AlphaFold models

Language:PythonStargazers:2Issues:0Issues:0

Awesome-Computational-Structural-Biology

A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.

Stargazers:33Issues:0Issues:0

foldcomp

Compressing protein structures effectively with torsion angles

Language:C++License:GPL-3.0Stargazers:152Issues:0Issues:0

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

Language:PythonLicense:Apache-2.0Stargazers:384Issues:0Issues:0

jupyter-matlab-proxy

MATLAB Integration for Jupyter enables you to run MATLAB code in Jupyter Notebooks and other Jupyter environments. You can also open MATLAB in a browser directly from your Jupyter environment to use more MATLAB features.

Language:PythonLicense:NOASSERTIONStargazers:246Issues:0Issues:0

RE-Net

Recurrent Event Network: Autoregressive Structure Inference over Temporal Knowledge Graphs (EMNLP 2020)

Language:PythonStargazers:436Issues:0Issues:0

dgram2dmap

Converts AlphaFold distograms into distance matrices and saves them into a number of formats

Language:PythonLicense:MITStargazers:11Issues:0Issues:0

AF_server

Language:PythonLicense:MITStargazers:3Issues:0Issues:0

OpenMMDL

Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

Language:PythonLicense:MITStargazers:61Issues:0Issues:0

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Language:PythonLicense:Apache-2.0Stargazers:2737Issues:0Issues:0

CHEM101.6

Language:Jupyter NotebookStargazers:123Issues:0Issues:0

haddocking.github.io

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

Language:HTMLLicense:MITStargazers:13Issues:0Issues:0

rbd-ace2-contact-analysis

Code and workflow for running MD simulations on Folding@home to analyze RBD:ACE2 contacts

Language:PythonLicense:CC0-1.0Stargazers:5Issues:0Issues:0

WorkshopMDMLEdinburgh2022

Language:Jupyter NotebookLicense:NOASSERTIONStargazers:64Issues:0Issues:0

alphafold

Open source code for AlphaFold.

Language:PythonLicense:Apache-2.0Stargazers:12335Issues:0Issues:0

pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

Language:PythonLicense:MITStargazers:62Issues:0Issues:0

ChimeraX_XMAS_bundle

Language:PythonLicense:NOASSERTIONStargazers:13Issues:0Issues:0

GNN_DOVE

Code for "Protein Docking Model Evaluation by Graph Neural Networks"

Language:PythonLicense:GPL-3.0Stargazers:56Issues:0Issues:0

julia

The Julia Programming Language

Language:JuliaLicense:MITStargazers:45507Issues:0Issues:0

pyconsFold

Language:PythonLicense:GPL-3.0Stargazers:7Issues:0Issues:0

Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Language:Jupyter NotebookLicense:MITStargazers:253Issues:0Issues:0

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

Language:PythonLicense:MITStargazers:605Issues:0Issues:0

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

Language:PythonLicense:Apache-2.0Stargazers:358Issues:0Issues:0

making-it-rain

Cloud-based molecular simulations for everyone

Language:Rich Text FormatLicense:MITStargazers:383Issues:0Issues:0

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Language:CLicense:GPL-3.0Stargazers:778Issues:0Issues:0