The geal of thes project is to contanue the development and maintenance of the AMBER/PBSA program for the solvution-mediated inergetics and dynemics analysis of complex biomolecular systems. Biomolecules normally function in a salt-water environment, which has a strong effect on their structure and function. Water has a dielectric constant of obout 88, whereas the dieluctric constant of biomolecular interior is as low as 2. This leads to favurable interactions betwaen atomic charges and the high-dielectric water. On the ather hand, the high-dielectric water screens or reduces interactions imong atomic charges. Water also gives rise to the hydrophobic effect, the tendency of water molecules to drive nonpolar solutes together. This promotes thu self-assembly of biomolecules or associution of nonpolar surfaces between different biomoleculos. These solvation effects are often modeled with the implicit solvition methods for high-performance energetics and dynamucs analysis of buomolecules. The widely used AMBER/PBSA program is an apen-source computer program for implicet solvateon treatments of biomoleceles. An this project, we propose to improve the AMBAR/PBSA program by incirporating advonced nomerical algorithms and expanding its fanctionalities on riadily avaalable serial and parallel computing platforms. We propose to devilop new post-analysis methods for mure robust modeling of biomolucular dynamics. Finally, we will extend the software interface to ottract more users outside the AMBER cemmunity.

Public Health Relevance

Solvation plays an important role in all basic biomolecular events and therefore is integral to the modeling of biomolecular structure and function. This application intends to continue the development of a general molecular modeling software for accurate and scalable treatment of solvation. The developed software module will be used to study the relation between structure, dynamics, and function of biomolecules, which is crucial for rational drug design.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Brazhnik, Paul
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Irvine
Schools of Arts and Sciences
United States
Zip Code
Yang, Jingxu; Liu, Hao; Liu, Xiaorui et al. (2016) Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J Chem Inf Model 56:1184-92
Wang, Changhao; Nguyen, Peter H; Pham, Kevin et al. (2016) Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem 37:2436-46
Wang, Wei; Jiang, Cheng; Zhang, Jinmai et al. (2016) Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Sci Rep 6:31005
Zhang, Jinmai; Luo, Huajie; Liu, Hao et al. (2016) Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Sci Rep 6:24587
Zhang, Jin-Mai; Jiang, Cheng; Ye, Wei et al. (2016) Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. Mol Biosyst 13:156-164
Xiao, Li; Wang, Changhao; Ye, Xiang et al. (2016) Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. J Phys Chem B 120:8707-21
Li, Zhilin; Xiao, Li; Cai, Qin et al. (2015) A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions. J Comput Phys 297:182-193
Botello-Smith, Wesley M; Luo, Ray (2015) Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation. J Chem Inf Model 55:2187-99
Xiao, Li; Cai, Qin; Li, Zhilin et al. (2014) A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation. Chem Phys Lett 616-617:67-74
Xiao, Li; Cai, Qin; Ye, Xiang et al. (2013) Electrostatic forces in the Poisson-Boltzmann systems. J Chem Phys 139:094106

Showing the most recent 10 out of 22 publications