Environment and exposure to solvent of protein atoms. Lysozyme and insulin.

By A. Shrake, J. A. Rupley. 1973

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Citations in the corpus

Improvement of molecular-replacement models with Sculptor (2011, methodology): “Sculptor implements a simple algorithm described by Shrake & Rupley (1973) in which the surface of each atom is approximated by a spherical mesh and each point in the mesh is checked for overlap with every other atom in the structure.”
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. (1999, background): “Probe produces dots that are always at the van der Waals surface of some atom, whereas solvent accessibility is classically measured out on the surface traced by the center of a 1.4 A Ê radius probe (Lee & Richards, 1971; Shrake & Rupley, 1973).”
KLIFS: a structural kinase-ligand interaction database (2015, unknown): “model derived from systematic analysis of the Accessible Surface Area (ASA) (32) of kinase binding site residues and vectors defining the directionality of DxDFG.”
Protein docking using spherical polar Fourier correlations (2000, methodology): “Here, these surfaces are estimated using our own algorithm 47 which is an adaptation of Shrake and Rupley’s 48 method of calculating solvent-accessible dot surfaces.”
Solvent accessible surface area approximations for rapid and accurate protein structure prediction (2009, methodology): “The Shrake and Rupley algorithm [38] involves the testing of points on an atom ’ s van der Waals surface for overlap with points on the van der Waals surface of neighboring atoms.”
GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome (2015, methodology): “where S(ri) is the accessible surface area of the ith atom of the structure which is calculated using the Shrake-Rupley algorithm (Shrake and Rupley, 1973) with ri being the van der Waals radius.”
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures (2008, methodology): “Both the SASA and exterior envelope elimination are calculated using the Shrake-Rupley dot-density method [5].”
Five computational developability guidelines for therapeutic antibody profiling (2019, methodology): “5%, compared with alanine-X-alanine for each residue X (23, 24).”