POPS

POPS calculates solvent-accessible surface areas at atomic and residue levels using an analytically parameterized formula to approximate the first solvation shell for applications such as integration into molecular dynamics simulations.

Key Features:

• Analytical formula (POPS-A and POPS-R): Uses a simple, empirically parameterized analytical formula to compute solvent-accessible surface areas at atomic (POPS-A) and residue (POPS-R) levels for rapid, accurate approximation compared with all-atom methods.
• Residue-level optimization: Models residue areas with single spheres centered on the C(alpha) atom for amino acids and the P atom for nucleotides, with parameters optimized against accurate all-atom calculations.
• First solvation shell approximation and MD integration: Provides an approximation of the first solvation shell suitable for integration into molecular dynamics simulations.
• Application to macromolecular assemblies: The residue-based POPS-R approach is tailored for large assemblies such as ribosomes and for refining low-resolution structures and identifying interactions within subunits and at interfaces.
• Conformational analysis: Detects conformational changes upon complex formation (for example with P-tRNA) and reveals exposure of specific residues such as Arg and Lys to negatively charged binding sites.
• Free energy estimations: Estimates loss of free energy of solvation upon complex formation to inform the design of protein-RNA and protein-protein complexes.

Scientific Applications:

• Structural refinement: Refinement of low-resolution structures of large macromolecular assemblies, including ribosomes.
• Molecular dynamics simulations: Fast solvation-area estimates usable within molecular dynamics workflows to assess solvation effects and interactions.
• Complex design: Estimation of solvation free-energy changes to support rational design of protein-protein and protein-nucleic acid complexes.

Methodology:

Analytical formula parameterized empirically from a diverse dataset of proteins and nucleic acids and optimized against all-atom calculations, with residue areas modeled as single spheres centered on C(alpha) for amino acids and the P atom for nucleotides.