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

The ProLint Webserver

The Website of the Ramiréz Lab

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

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 .

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.

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

Map the depth on a PDB file

Source code for building the EncoMPASS database

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

Membrane alpha helix packing and orientation predicrtor

Membrane helix prediction with SVMs

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

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

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

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

Documentation

uwseds-group-OPMxplore created by GitHub Classroom

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