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protein-inference

A python package for protein inference in Mass Spectrometric data analysis.

protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations

protein-quality-gn

Protein quality assessment using Graph Convolutional Networks

protein-science

A collection of useful tutorials for Protein Science

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

protein-transformer

Predicting protein structure through sequence modeling

protein_dcgan

proteindescriptor

a protein descriptor for site prediction

proteingan

proteinnet

Standardized data set for machine learning of protein structure

proteinsolver

Generate new protein sequences using graph neural networks.

proteinstatsai

Prediction of protein statistics and properties using neural networks.

proteome_prediction

proteomedigestsim

A collection of R classes to allow prediction of proteome coverage based on digestion, specifically iterative digestion by MED-FASP

proteomics

useful functions for analysis of proteomic data

proteomics_data_mining_challenge

proteotorch

Deep learning and ultrafast machine learning for peptide identification of shotgun proteomics data.

protocaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

prottrans

ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

psearch

3D ligand-based pharmacophore modeling

psikit

psi4+RDKit

psims

A declarative API for writing XML documents for HUPO PSI-MS mzML and mzIdentML

pspd_minimization

A comparison of several minimization methods in Rosetta. Final project in Protein Structure Prediction and Design (JHU 19SP)

pubchem-utils

Utilities for interacting with PubChem

publications

Supporting information of publications from Structural Bioinformatics Group

pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

py4chemoinformatics

Draft of Python for chemoinformatics

pyberny

Molecular structure optimizer

pybiomed

machine learning, molecular descriptor

pycadd

A python package for computer-aid drug design.