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Unique identifier OMICS_17039
Name ODA
Alternative name Optimal Docking Area
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

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Publication for Optimal Docking Area

ODA citations

 (10)
library_books

A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison

2017
Proteins
PMCID: 5396268
PMID: 27935158
DOI: 10.1002/prot.25218

[…] mely C2_Q1_N_CP_D1 (rank 2), C2_AVG_N_CP_D1 (rank 5), C2_MIN_N_CP_D1 (rank 6), C1_MIN_N_CP_D1 (rank 8), C2_Q3_N_CP_D1 (rank 12), C1_Q1_N_CP_D1 (rank 20). Other molecular descriptors in the top 20 are optimal docking area (N_ODA, se), PIE score (N_CP_PIE, cs), SIPPER (N_SIPPER, cs), w_local Z‐score C_beta potential (N_CP_ZLOCAL_CB, sp), FireDock energy (N_FIREDOCK, cs) and the PISA score (N_AP_PISA […]

library_books

The structure function of the death domain of human IRAK M

2014
PMCID: 4273448
PMID: 25481771
DOI: 10.1186/s12964-014-0077-3

[…] A consensus approach was used to predict protein-protein interactions for the model structure generated by application of several structural bioinformatics methods. We employed: Optimal Docking Area (ODA) [], Cons-PPISP [] and PPI-Pred []. For each of these methods, a prediction score was obtained for all residues in the death domain of IRAK-M and a consensus was generated fr […]

library_books

Understanding the functional difference between growth arrest specific protein 6 and protein S: an evolutionary approach

2014
Open Biol
PMCID: 4221892
PMID: 25339693
DOI: 10.1098/rsob.140121

[…] GAS6 residues (PDB ID: 2C5D) involved in protein–protein interactions were predicted with the Optimal Docking Area (ODA) program from the ICM Pro package (Molsoft) []. […]

library_books

Computational prediction of protein protein complexes

2012
BMC Res Notes
PMCID: 3599296
PMID: 22958278
DOI: 10.1186/1756-0500-5-495

[…] e energies. ClusPro then generates cluster centers that are a representative set of complexes that form a cluster. The cluster centers are ranked according to cluster sizes.MetaPPISP [] and Molsoft’s Optimal Docking Area (ODA) [] tools are used to predict the interfacial residues in a protein-protein complex. These two softwares are based on different algorithms and a consensus interface generated […]

library_books

LRR Conservation Mapping to Predict Functional Sites within Protein Leucine Rich Repeat Domains

2011
PLoS One
PMCID: 3138743
PMID: 21789174
DOI: 10.1371/journal.pone.0021614

[…] t predict important amino acid residues within a protein, beyond the BLAST or Pfam-like methods that identify conserved motifs in the primary sequence, include positive/purifying selection analysis , optimal docking area (ODA) calculation , and Consurf . Because these three approaches employ different criteria for identifying functionally significant residues, we searched for important residues of […]

library_books

Defining the Functional Domain of Programmed Cell Death 10 through Its Interactions with Phosphatidylinositol 3,4,5 Trisphosphate

2010
PLoS One
PMCID: 2909203
PMID: 20668527
DOI: 10.1371/journal.pone.0011740

[…] Protein-protein interface sites were identified by applying the optimal docking area method (ODA; ), which segregates surface patches and applies atomic desolvation calculations parameterized with octanol/water transfer experiments […]

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ODA institution(s)
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA, USA; Molsoft, LLC, La Jolla, CA, USA

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