Ameya Harmalkar

发表

Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features

Jeffrey J. Gray, J. J. Gray, Roshan Rao, 2022, bioRxiv.

Advances to tackle backbone flexibility in protein docking.

Jeffrey J. Gray, Jeffrey J. Gray, Ameya Harmalkar, 2020, Current opinion in structural biology.

Molecular dynamics simulation for desulphurization of hydrocarbon fuel using ionic liquids

S. Prabhu, Shashank K. Bhangde, Ameya Harmalkar, 2018 .

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Jeffrey J. Gray, Panagiotis I. Koukos, Johnathan D. Guest, 2021, Proteins.

Induced fit with replica exchange improves protein complex structure prediction

Jeffrey J. Gray, J. J. Gray, S. Mahajan, 2021, bioRxiv.

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Jeffrey J. Gray, S. Mohammed, J. J. Gray, 2021, bioRxiv.

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

Jeffrey J. Gray, Jeffrey A. Ruffolo, J. J. Gray, 2023, bioRxiv.

Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

Jeffrey J. Gray, Sergey Lyskov, Ameya Harmalkar, 2023, bioRxiv.

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

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features

Jeffrey J. Gray, Roshan Rao, C. Tinberg, 2023, mAbs.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Johnathan D. Guest, Adam K. Sieradzan, Charles W Christoffer, 2023, Proteins.

Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta

Rituparna Samanta, Ameya Harmalkar, Jeffrey J. Gray, 2024, bioRxiv.