Ali Saglam
Affiliations: | 2012- | Chemistry | University of Pittsburgh, Pittsburgh, PA, United States |
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| Husar A, Ordyan M, Garcia GC, et al. (2024) MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. Plos Computational Biology. 20: e1011800 |
| Bogetti AT, Leung JMG, Russo JD, et al. (2023) A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. Living Journal of Computational Molecular Science. 5 |
| Shaikh B, Smith LP, Vasilescu D, et al. (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research |
| Bogetti AT, Mostofian B, Dickson A, et al. (2019) A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. Living Journal of Computational Molecular Science. 1 |
| Tapia JJ, Saglam AS, Czech J, et al. (2019) MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods in Molecular Biology (Clifton, N.J.). 1945: 203-229 |
| Saglam AS, Chong LT. (2019) Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations. Chemical Science. 10: 2360-2372 |
| Saglam AS, Wang D, Zwier MC, et al. (2017) Flexibility vs. Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues. The Journal of Physical Chemistry. B |
| Chong LT, Saglam AS, Zuckerman DM. (2016) Path-sampling strategies for simulating rare events in biomolecular systems. Current Opinion in Structural Biology. 43: 88-94 |
| Saglam AS, Chong LT. (2015) Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models. The Journal of Physical Chemistry. B |