CASTp: Computed Atlas of Surface Topography of proteins

By T. Binkowski, S. Naghibzadeh, Jie Liang. Nucleic Acids Res., 2003

2,124 citations recorded by the source corpus.

Subfields: Cell Biology, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eb1c05fb078c92974285b263562886fddcd3eab5

How researchers see this paper

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

In Cell Biology

In Materials Chemistry

In Molecular Biology

Citations in the corpus

CASTp 3.0: computed atlas of surface topography of proteins (2018, positive): “The CASTp server aims to provide comprehensive and detailed quantitative characterization of topographic features of proteins [4, 5].”
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues (2006, methodology): “We will then describe updates to the CASTp (2,3) web server for visualization of the annotated functional residues, with emphasis on mapping to surface pockets and interior voids.”
MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction (2009, neutral): “CAST is not taken into account in metaPocket because it identiﬁes the protein atoms forming a pocket rather than the probes around the pocket sites.”
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation (2006, positive): “CAST is not evaluated since we only get a Pymol plugin for it, which has to be used manually.”
High resolution X‐ray structures of mouse major urinary protein nasal isoform in complex with pheromones (2010, methodology): “0)59 and CASTp.60 Figures were generated using PyMol (v0.”
The Structure, Stability and Pheromone Binding of the Male Mouse Protein Sex Pheromone Darcin (2014, methodology): “The CASTp programme [46] was used to measure cavity size and the programmes PIC [47], PDBePISA [48] and LIGPLOT [49] measured intramolecular hydrophobic and ionic contacts.”
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure (2009, methodology): “LigsiteCS, Q-SiteFinder, and CASTp.”
The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins (2015, methodology): “This category includes methods such as POCKET 56 , LIGSITE 57,58 , PASS 59 and CASTp 60 .”
Advances in Protein Chemistry and Structural Biology (2010, methodology): “We can rapidly query a protein surface pocket against CASTp database through alignment of sequence fragments using standard dynamic programming technique, allowing gap insertion (Binkowski et al., 2003a).”
Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane. (2016, methodology): “The CASTp (Computed Atlas of Surface Topology of Proteins) server (Dundas et al., 2006) was employed to calculate the surface area and binding sites of the ALS catalytic site in both the VAT1 bound (activated and inhibited) and unbound states to determine the overall effect of VAT1 binding on the ac”
Predicting protein function from sequence and structural data. (2005, methodology): “The pvSOAR [21 ] web server allows searches to be performed against the CASTp [22] database or against non-redundant PDB data sets.”
PocketPicker: analysis of ligand binding-sites with shape descriptors (2007, methodology): “The program CAST [8,9] uses an approach based on alpha shapes [10,11] and triangulations of complex shapes.”