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pdbfixer

PDBFixer fixes problems in PDB files

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

pdynamo-mirror

Mirror of pDynamo computational chemistry library

penncnv

Copy number vaiation detection from SNP arrays

pepevolve

Evolutionary algorithm to generate offspring of one or morph two (peptide) sequences into each other

peptide_design

Tools that enable de novo design of protein-binding peptides

peptidebuilder

A simple Python library to generate model peptides

peptidedesignga

peptides.py

Physicochemical properties, indices and descriptors for amino-acid sequences.

peptimizer

Peptide optimization with Machine Learning

performance

GAMESS Performance Benchmark

performer-pytorch

An implementation of Performer, a linear attention-based transformer, in Pytorch

pesnet

Reference implementation of "Ab-Initio Potential Energy Surfaces by Pairing GNNs with Neural Wave Functions" (ICLR, 2022)

pgmpy

Python Library for Probabilistic Graphical Models

pharmacokinetic_prediction

Prediction of intravenous pharmacokinetic parameters, including fu, MRT, t1/2, VD and CL, by training on 1352 compounds.

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

phd-thesis

Repository of my thesis "Understanding Random Forests"

phen2gene

Phenotype driven gene prioritization for HPO

photo-labeling

pinet

pinn

a Python library for building atomic neural networks

pipeline-tools

Pipeline-tools for HCA DCP Secondary Analyses Service

pk_model

Pharmacokinetic model developed by students on the Oxford Interdisciplinary Bioscience DTP. Focus on comparing solutions to different models/dosing protocols.

pkdb1

Pharmacokinetics database

pks-enumerator

PKS Enumerator is a cheminformatics tool to generate virtual chemical libraries of macrocycles or macrolides. The innovation of our enumeration approach relies on its ability to create extremely large and diverse chemical libraries by manipulating and constraining key structural parameters of the enumerated compounds, such as the type, number, and redundancy of structural motifs in each compound or the overall diversity of the library.

playground

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

pmda

Parallel algorithms for MDAnalysis

pnet_prostate_paper

P-NET, Biologically informed deep neural network for prostate cancer classification and discovery

pocket2drug

A generative deep learning model to predict binding drugs for protein ligand-binding sites.