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perses

Experiments with expanded ensembles to explore chemical space

pfbde.jl

Code Examples from Parameter Free Bayesian Density Estimation by P. Richard Hahn (2016) [http://faculty.chicagobooth.edu/richard.hahn/PFBDE.pdf]

pfocal

Fast parallel convolution in R.

pharmr

R wrapper to pharmpy

phbuilder

Scripts related to building and analysing constant-pH MD simulations in Gromacs

phd-commits

Functions for scraping git commits from repositories associated with a PhD (or anything else) and plotting them.

phd-python-scripts

the scripts I used for data processing and run control of GROMACS on a linux system

phillydaodata

physical_validation

Physical validation of molecular simulations

pic

Direct Coupling Analysis

pida

Software for analyzing multiple protein-protein interaction docking solutions, calculating contact regions using mdtraj, and visualizing in useful ways via nglview.

pidginv2

PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (OLD VERSION: https://github.com/lhm30/PIDGIN)

piex

Pipeline Explorer - Explore and analyze millions of pipelines learned using MLBlocks and MLPrimitives.

pingr

ICMP and TCP ping and related tools

pipelearner

Tidy machine learning pipelines

pipeline-singlecellrnaseq

Custom pipeline to preprocess the raw sequencing data for a single cell/nuclei transcriptomic profiling

pipelines

NGS pipelines for ChIP-Seq, RNA-Seq and scRNA-Seq data

piton

Parsing Expression Grammars for Rcpp

pixeldb

pkai

pKAI: a fast and interpretable deep learning approach to accurate electrostatics-driven pKa prediction

pkg-dev-tutorial

Package Development tutorial for useR! 2019 Toulouse

pkg_primer

R package primer: a minimal tutorial on writing R packages

pkpdb

Download the database content @ https://pkpdb.pypka.org

pkpdsim

Simulate PK-PD models defined as ODE systems

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.

platemo

Evolutionary multi-objective optimization platform

playground

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

plotly.py

The interactive graphing library for Python (includes Plotly Express) :sparkles:

plpth813bioinformatics