PRISM protocols

PRISM specifications

Information


Unique identifier OMICS_03648
Name PRISM
Alternative name Protein Interactions By Structural Matching
Interface Web user interface
Restrictions to use None
Input data Two protein structures
Input format PDB
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Attila Gursoy <>

Publications for Protein Interactions By Structural Matching

PRISM IN pipelines

 (4)
2016
PMCID: 5100575
PMID: 27604871
DOI: 10.1093/nar/gkw770

[…] half of the simulation frames were considered. the psn, lmi and psn-lmi calculations were performed using wordom (62). we mapped the paths on the 3d structures by the xpyder (63) plugin for pymol., prism is a motif-based software to predict protein-protein interactions (64). it includes a rigid-body structural comparison of target proteins to known templates of protein–protein interfaces […]

2016
PMCID: 5100575
PMID: 27604871
DOI: 10.1093/nar/gkw770

[…] (64). it includes a rigid-body structural comparison of target proteins to known templates of protein–protein interfaces and a flexible refinement using a docking energy function. we employed prism (64,65) to screen 54 different potential interaction partners for the p53 dbd. we used 40 conformations of p53 dbd from our simulations, including both the dna-bound and -unbound states, along […]

2016
PMCID: 5100575
PMID: 27604871
DOI: 10.1093/nar/gkw770

[…] each pca substate and they were subjected to energy minimization with the steepest descent algorithm. the potential interaction partners selected in the first round step were then re-submitted to prism2.0 and evaluated on the basis of their docking energy scores considering an energy value cutoff of −2.39 kcal/mol for favourable interactions, as previously suggested by the developers […]

2016
PMCID: 5100575
PMID: 27604871
DOI: 10.1093/nar/gkw770

[…] basis of their docking energy scores considering an energy value cutoff of −2.39 kcal/mol for favourable interactions, as previously suggested by the developers of the method (64). to benchmark our prism analyses, we performed calculations using four crystallographic structures of p53 dbd obtained in presence or absence of dna and known p53 partners for which experimental data of the complexes […]

PRISM institution(s)
Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
PRISM funding source(s)
National Cancer Institute, National Institutes of Health (NIH) [HHSN261200800001E] (whole or in part); Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research (in part); Scientific and Technological Research Council of Turkey (TUBITAK) [113E164]

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