CASTp statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CASTp
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Tool usage distribution map

This map represents all the scientific publications referring to CASTp per scientific context
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Associated diseases

This word cloud represents CASTp usage per disease context
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Popular tool citations

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Protocols

CASTp specifications

Information


Unique identifier OMICS_08121
Name CASTp
Interface Web user interface
Restrictions to use None
Input format PDB
Output data You will receive five files in email for the calculated results: pocket information file, pocket atoms, mouth atoms, and a script file for visualization using rasmol.
Computer skills Basic
Stability Stable
Maintained Yes

Publications for CASTp

CASTp citations

 (222)
library_books

Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

2018
PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] e, specifically the values for the active sites were much higher. This result suggests that pockets contribute to the prediction of binding sites, and active sites from protein structures. GHECOM and CASTp results are shown in and . […]

library_books

An allosteric inhibitor of Mycobacterium tuberculosis ArgJ: Implications to a novel combinatorial therapy

2018
PMCID: 5887547
PMID: 29483133
DOI: 10.15252/emmm.201708038

[…] ed our quest to discover a small molecule inhibitor of MtArgJ by investigating the protein surface. MtArgJ structure (PDB ID: 3IT6) was probed for surface cavity predictions (by MetaPocket server and CastP analysis) and a well‐defined pocket of area 2,019.7 Å2 and volume 3,104.8 Å3 located in‐between the two active sites was discovered (Fig A). This pocket comprises of 48% hydrophobic amino acid r […]

call_split

Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly amongst IspD/IspE/IspF enzymes in the MEP pathway

2018
Biosci Rep
PMCID: 5821942
PMID: 29335298
DOI: 10.1042/BSR20171370
call_split See protocol

[…] The cavity analysis was performed using CASTp server [], surface calculations were performed by ArealMol from CCP4 programs suite []. […]

library_books

Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU S2B, a Key Enzyme in the “4S” Desulfurization Pathway

2018
Front Microbiol
PMCID: 5819316
PMID: 29497411
DOI: 10.3389/fmicb.2018.00231

[…] y component of the active pocket, which, along with IS1, IS2, and IS3, controls the size of the pocket. The volume of the active pocket of BdsA, and those of homologous proteins, are calculated using CASTp server (). The volume of the BdsA activity pocket is 5134.9 Å3. Nitrilotriacetate monooxygenase catalyzes the degradation of the nitrilotriacetate substrate, with the active pocket volume of 528 […]

call_split

The structure of FIV reverse transcriptase and its implications for non nucleoside inhibitor resistance

2018
PLoS Pathog
PMCID: 5798851
PMID: 29364950
DOI: 10.1371/journal.ppat.1006849
call_split See protocol

[…] ted using ESPript []. PyMOL Molecular Graphics System (Schrödinger, LLC) was used for preparing structural figures and for structural superposition. Comparative pocket volumes were analyzed using the CASTp server [] using HIV-1 RT bound to NVP without nucleic acid (PDB code: 5HBM) or bound to NVP with nucleic acid (PDB code: 4PUO). Both HIV-1 RT structures show comparable volumes validating the us […]

library_books

Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region

2018
Sci Rep
PMCID: 5772511
PMID: 29343701
DOI: 10.1038/s41598-017-19075-2

[…] ajectory file in VMD program. Binding pocket calculation was performed for wild-type and alanine mutants after the removal of ATP from the PS-ATP complex (PDB ID: 2a84) at the interval of 10 ns using CASTp server. […]


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CASTp institution(s)
Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA

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