| A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0] AT Bogetti, B Mostofian, A Dickson, AJ Pratt, AS Saglam, PO Harrison, ... Living journal of computational molecular science 1 (2), 2019 | 810 | 2019 |
| Path-sampling strategies for simulating rare events in biomolecular systems LT Chong, AS Saglam, DM Zuckerman Current opinion in structural biology 43, 88-94, 2017 | 116 | 2017 |
| Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations AS Saglam, LT Chong Chemical science 10 (8), 2360-2372, 2019 | 80 | 2019 |
| Iterative community-driven development of a SARS-CoV-2 tissue simulator M Getz, Y Wang, G An, M Asthana, A Becker, C Cockrell, N Collier, ... BioRxiv, 2020.04. 02.019075, 2021 | 56 | 2021 |
| Highly Efficient Computation of the Basal kon using Direct Simulation of Protein–Protein Association with Flexible Molecular Models AS Saglam, LT Chong The Journal of Physical Chemistry B 120 (1), 117-122, 2016 | 38 | 2016 |
| BioSimulators: a central registry of simulation engines and services for recommending specific tools B Shaikh, LP Smith, D Vasilescu, G Marupilla, M Wilson, E Agmon, ... Nucleic acids research 50 (W1), W108-W114, 2022 | 24 | 2022 |
| Flexibility vs preorganization: Direct comparison of binding kinetics for a disordered peptide and its exact preorganized analogues AS Saglam, DW Wang, MC Zwier, LT Chong The Journal of Physical Chemistry B 121 (43), 10046-10054, 2017 | 23 | 2017 |
| MCell-R: A particle-resolution network-free spatial modeling framework JJ Tapia, AS Saglam, J Czech, R Kuczewski, TM Bartol, TJ Sejnowski, ... Modeling Biomolecular Site Dynamics: Methods and Protocols, 203-229, 2019 | 20 | 2019 |
| Combination treatment optimization using a pan-cancer pathway model R Schmucker, G Farina, J Faeder, F Fröhlich, AS Saglam, T Sandholm PLOS Computational Biology 17 (12), e1009689, 2021 | 13 | 2021 |
| A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0. 1] AT Bogetti, JMG Leung, JD Russo, S Zhang, JP Thompson, AS Saglam, ... bioRxiv, 2022.10. 04.510803, 2022 | 10 | 2022 |
| Mcell4 with bionetgen: A Monte Carlo simulator of rule-based reaction-diffusion systems with python interface A Husar, M Ordyan, GC Garcia, JG Yancey, AS Saglam, JR Faeder, ... PLOS Computational Biology 20 (4), e1011800, 2024 | 9 | 2024 |
| WEBNG: A templating tool for weighted ensemble sampling of rule-based models AS Saglam, JR Faeder bioRxiv, 2022.10. 28.514312, 2022 | | 2022 |
| Molecular Simulations of Pathways and Kinetics for Protein-Protein Binding Processes AS Saglam University of Pittsburgh, 2018 | | 2018 |