CASTp 3.0: computed atlas of surface topography of proteins

By Wei Tian, Chang Chen, X. Lei, Jieling Zhao, Jie Liang. Nucleic Acids Res., 2018

2,078 citations recorded by the source corpus.

Abstract Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/f0d9ec4b725b5dcdb7ef4a4e05cded12b18e182a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Po-Ssu Huang
2. David Baker
3. Yang Zhang
4. Tanja Kortemme
5. Jeffrey J. Gray
6. Jens Meiler
7. I. Samish
8. Sergey Ovchinnikov

In Molecular Biology

1. Po-Ssu Huang
2. David Baker
3. M. J. Bick
4. I. Samish
5. Tanja Kortemme
6. Yang Zhang
7. Jeffrey J. Gray
8. Xingjie Pan

In Spectroscopy

1. Po-Ssu Huang
2. David Baker
3. Oliver F. Lange

Citations in the corpus

• Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. (2019, background): “0 (Tian et al., 2018) analysis revealed a solvent-accessible volume of 23.”
• Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion (2020, methodology): “Structure illustrations were prepared with PyMOL (47), while estimates of volume of enclosed cavity were obtained using the CASTp server (48), based upon models with bulk solvent-accessible channels plugged with dummy atoms.”