chenshengsgithub Goto Github PK

3d-resnets-pytorch

3D ResNets for Action Recognition (CVPR 2018)

3dunetcnn

Pytorch 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation

aixfuse

alchemy

alphafold

Open source code for AlphaFold.

blast-bioinfor-tool

Python implementation of Basic Local Alignment Search Tool (BLAST) , which is the core algorithm in sequence alignment for genomes.

blog

camp

predicting peptide-protein interactions

cdhit

Automatically exported from code.google.com/p/cdhit

chenshengsgithub.github.io

controlled-peptide-generation

source code for https://arxiv.org/abs/2005.11248 "Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics"

coulomb_matrix

A Python based code to construct a Sorted Coulomb matrix from Smile strings (CSV input) of molecules . An optional scikit-learn is invoked at the end of the script to classify molecules using SVM.

deepfri

Deep functional residue identification

dms_opt

easy_af2

Easy to AF2

emodelx

emodelx_new

emodelx_old

fold2seq

Code for Fold2Seq paper from ICML 2021

gh-icp

GH-ICP: Iterative Closest Point algorithm with global optimal matching and hybrid metric [3DV' 18]

gnn_dti

gvp

Geometric Vector Perceptron --- a rotation-equivariant GNN for learning from biomolecular structure

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

hsm

Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."

ic_gan

Official repository for the paper "Instance-Conditioned GAN" by Arantxa Casanova, Marlene Careil, Jakob Verbeek, Michał Drożdżal, Adriana Romero-Soriano.

ifeature

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.

ilearnplus

iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.

masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

mcts

A simple package to allow users to run Monte Carlo Tree Search on any perfect information domain

mmtf

The specification of the MMTF format for biological structures