Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories.

The ProLint Webserver

A software for membrane analysis and subtraction in cryo-EM.

The Website of the Ramiréz Lab

A software for membrane analysis and subtraction in cryo-EM.

A Python package designed for analyzing the internal degrees of freedom within molecular structures, focusing particularly on membrane proteins. It conducts statistical analyses, providing deep insights into the dynamics and flexibility of molecular interactions. Ideal for finding the most flexible regions within a protein.

A small Python package to set up electrostatic solvation free energy ("Born energy") calculations of an ion in a membrane protein and calculate the electrostatic free energy with APBS .

Map the depth on a PDB file

Dataset of the "Integrative Modeling of Membrane-associated Protein Assemblies" manuscript

Code for the manuscript "Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction".

Source code for building the EncoMPASS database

Membrane alpha helix packing and orientation predicrtor

Membrane helix prediction with SVMs

A statistical model to predict heterologous membrane protein expression in E. coli!

Calculation of cross sectional area profiles from MD simulations of membrane proteins.

A gromacs tutorial for creating a gromos54A7 simulation system of a protein in a simple membrane

TooT-PLM-ionCT: A bioinformatics framework utilizing protein language models for accurate classification of ion channels and ion transporters from membrane proteins.

Documentation

uwseds-group-OPMxplore created by GitHub Classroom

a database of membrane binding sites in intrinsically disordered regions of human transmembrane proteins