Vikram Khipple Mulligan

Heuristic energy-based cyclic peptide design

This paper introduces CyclicChamp, a computational pipeline for designing cyclic peptides of 7-24 residues, achieving stable designs validated by molecular dynamics simulations.

CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Conformational Sampling

CyclicCAE generates energetically favorable macrocycle conformations faster than Rosetta's GeneralizedKIC, using synthetic data and enabling design and structure prediction.

The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design

The paper introduces Masala, an open-source software suite designed to extend and improve upon Rosetta for synthetic heteropolymer design, offering modular architecture and performance improvements.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

The paper presents a framework for ensuring reproducibility in bio-macromolecular modeling through automated benchmarks and a test server, demonstrating its utility for Rosetta and other tools.

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

XENet improves protein design on quantum computers by reducing rotamer counts and problem size through enhanced graph convolution.