kalininalab Goto Github PK

alpar

Single Reference Antimicrobial Resistance

alphafold_non_docker

AlphaFold2 non-docker setup

compressbinarytable

Compresses binary tables

d-structman

data-versioning-examples

Examples of data stored under version control systems & list of various resources for data stewardship

datasail

DataSAIL is a tool to split datasets while reducing information leakage.

datasail_tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

epipampas

Rapid detection of intra-protein epistasis via parsimonious ancestral state reconstruction and counting parallel mutations

glyles

A tool to convert IUPAC representations of glycans into SMILES strings.

graphdta_pdbbind

GraphDTA: Predicting drug-target binding affinity with graph neural networks on the PDBbind dataset

graphpli

Structure-informed Prediction of Interactions of Lectins and Glycans

lp-pdbbind

metaprofi

MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant genetic variants

naturalpplum

openfold_non_docker

OpenFold non-docker setup

panpa

PanPA is a tool for generating alignment of protein graphs

protpretrain

Protein structure pretraining

qcqp

A CVXPY extension for handling nonconvex QCQP via Suggest-and-Improve framework

rindti

rinminer

RINminer is a frequent subgraph mining tool based on the gSpan algorithm with additional features and optimizations for residue interaction networks (RINs).

scala

smtb2022

smtb_2023

spherecon

This tool calculates a measure for relative solvent accessible area for single residues or whole amino acid chains.

structman

useful_scripts

A repository to share our useful scripts in, between our group and others