Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
By Jian Yu, Yong Zhou, Isao Tanaka, Min Yao. Bioinform., 2010
355 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/76e1dcee27d9038f3b4be863c37d3fe37fd04f98
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- Petr Skoda
- Marián Novotný
- David Hoksza
- Radoslav Krivák
- Julio Caballero
- David Ramírez
- Daniele Toti
- Fabio Polticelli
In Molecular Biology
- Petr Skoda
- Marián Novotný
- Radoslav Krivák
- David Hoksza
- Julio Caballero
- David Ramírez
- Daniele Toti
- Fabio Polticelli
Citations in the corpus
- Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins (2021, positive): “The far right panel shows the solvent accessible cavity (red surface representation) identified with POCASA56 and the volume (Å3) of the largest identified cavity is indicated.”
- Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? (2018, methodology): “Binding site volumes were calculated considering a probe radius of the probe sphere of 1 Å, single point flag of 12, protein depth flag of 18, and grid size of 1 Å [47].”
- PrankWeb: a web server for ligand binding site prediction and visualization (2019, background): “Fpocket (2), SiteHound (3), ConCavity (4), POCASA (5), MetaPocket 2.”
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies (2019, methodology): “A point, once the contribution of all its neighboring points is computed, will be deemed a pocket or cavity point if its SPF value is higher than the SPF threshold that is assigned by the user or automatically adjusted by Roll.”