| Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 | 81 | 2021 |
| Advances to tackle backbone flexibility in protein docking A Harmalkar, JJ Gray Current opinion in structural biology 67, 178-186, 2021 | 45 | 2021 |
| Molecular dynamics simulation for desulphurization of hydrocarbon fuel using ionic liquids MB Singh, AU Harmalkar, SS Prabhu, NR Pai, SK Bhangde, VG Gaikar Journal of Molecular Liquids 264, 490-498, 2018 | 18 | 2018 |
| Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment MF Lensink, G Brysbaert, N Raouraoua, PA Bates, M Giulini, RV Honorato, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1658-1683, 2023 | 16 | 2023 |
| Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks J Koehler Leman, S Lyskov, SM Lewis, J Adolf-Bryfogle, RF Alford, ... Nature communications 12 (1), 6947, 2021 | 15 | 2021 |
| Colicin-mediated transport of DNA through the iron transporter FepA R Cohen-Khait, A Harmalkar, P Pham, MN Webby, NG Housden, ... MBio 12 (5), 10.1128/mbio. 01787-21, 2021 | 10 | 2021 |
| Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features A Harmalkar, R Rao, Y Richard Xie, J Honer, W Deisting, J Anlahr, ... Mabs 15 (1), 2163584, 2023 | 8 | 2023 |
| Induced fit with replica exchange improves protein complex structure prediction A Harmalkar, SP Mahajan, JJ Gray PLoS computational biology 18 (6), e1010124, 2022 | 8 | 2022 |
| Flexible protein–protein docking with a multitrack iterative transformer LS Chu, JA Ruffolo, A Harmalkar, JJ Gray Protein Science 33 (2), e4862, 2024 | 5 | 2024 |
| Conchú ir S Lyskov, FC Chou SO., Der, BS, Drew, K., Kuroda, D., Xu, J., Weitzner, BD, Renfrew, PD …, 2013 | 4 | 2013 |
| Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange A Harmalkar, S Lyskov, JJ Gray bioRxiv, 2023 | 2 | 2023 |
| Machine learning techniques for predicting thermostability A Harmalkar, KY Wei US Patent App. 18/195,155, 2023 | | 2023 |
| Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features AU Harmalkar, JJ Gray, K Wei Biophysical journal 122 (3), 145a, 2023 | | 2023 |
| Hamiltonian-Resolution Replica Exchange Improves Flexible Backbone Protein Docking By Mimicking Induced-Fit Pathways A Harmalkar, JJ Gray 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Coupling Replica Exchange with Backbone sampling Captures Conformational Changes on Protein-Protein Interfaces A Harmalkar, JJ Gray 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Directed Evolution of PDGFR-β and PDGF-BB for Promotion of Bone Regeneration. M Kizerwetter, E Leonard, A Harmalkar, A Horenberg, M Leff, W Grayson, ... 2021 AIChE Annual Meeting, 2021 | | 2021 |
| Replica Exchange and Backbone Sampling Methods Improve Protein-Protein Docking By Mimicking Induced-Fit Pathways A Harmalkar, SP Mahajan, JJ Gray 2021 AIChE Annual Meeting, 2021 | | 2021 |
| Coupling Enhanced Sampling with Monte Carlo Techniques Improves Flexible-Backbone Protein Docking A Harmalkar, J Gray 2020 Virtual AIChE Annual Meeting, 2020 | | 2020 |
Jeffrey J. GrayJohns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular BiophysicsVerified email at jhu.edu
