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

MCP-ANM/mANM with PRS for membrane tension & tethering

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

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

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

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

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

Membrane helix prediction with SVMs

Membrane alpha helix packing and orientation predicrtor

Source code for building the EncoMPASS database

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

MPLID (Membrane Protein-Lipid Interaction Database): A large-scale experimentally-validated dataset of residue-level protein-lipid contacts from 2,792 membrane protein structures.

Documentation