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DiMoVo specifications

Information


Unique identifier OMICS_17437
Name DiMoVo
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Julie Bernauer

Publication for DiMoVo

DiMoVo citations

 (7)
library_books

Spontaneous non canonical assembly of CcmK hexameric components from β carboxysome shells of cyanobacteria

2017
PLoS One
PMCID: 5608322
PMID: 28934279
DOI: 10.1371/journal.pone.0185109

[…] ched on a real protein dimer, the B. subtilis pyrimidine-biosynthetic operon repressor PyrR []. BMC-H interhexamer contacts are classified as biologically irrelevant by specialized algorithms such as DiMoVo, which was conceived to discern between specific and unspecific protein-protein interfaces revealed in crystal structures []. Indeed, surfaces buried between hexamers in 3D structures of BMC-H/ […]

library_books

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

2015
Bioinformatics
PMCID: 4743631
PMID: 26508758
DOI: 10.1093/bioinformatics/btv622

[…] class, appeared in 2006 and used six interface properties in a support vector machine three-state classifier distinguishing obligate, non-obligate and crystal packing interactions (). Another method, DiMoVo (), relied on Voronoi tessellation to obtain parameters for interface description and a support vector machine to achieve a two-state classification from those parameters. In the same year, the […]

library_books

A structural dissection of large protein protein crystal packing contacts

2015
Sci Rep
PMCID: 4572935
PMID: 26370141
DOI: 10.1038/srep14214

[…] difficult to distinguish from each other. To test the performance of the current computational methods on the large crystal packing contacts, four popular methods were selected including PITA, PISA, DiMoVo and EPPIC. shows that when predicting the interfaces for a set of 92 large crystal packing and 103 weak transient complexes, high error rates are observed in all of the methods. However, it is […]

library_books

Use B factor related features for accurate classification between protein binding interfaces and crystal packing contacts

2014
BMC Bioinformatics
PMCID: 4290652
PMID: 25522196
DOI: 10.1186/1471-2105-15-S16-S3

[…] is a novel idea to outperform the existing methods in distinguishing crystal packing from homodimers []. Using residue pairs to describe interfaces, Bernauer et al. have constructed an SVM classifier DiMoVo for identifying biological protein interactions []. Liu and Li have designed the propensity vector of residue contacts within the O-ring to develop OringPV for the distinction between crystal p […]

library_books

In Silico and In Vitro Studies on the Protein Protein Interactions between Brugia malayi Immunomodulatory Protein Calreticulin and Human C1q

2014
PLoS One
PMCID: 4153637
PMID: 25184227
DOI: 10.1371/journal.pone.0106413

[…] hese interactions are playing the vital role in formation of biological complex and stabilizing the complexes. To check the docked protein-protein complex as potential biological complex, we used the DiMoVo server . Potential biological complex was predicted using the SVM methods and values above 0.5 indicated that the complex obtained was biologically potent. We also checked the role of metal ion […]

call_split

Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces

2013
PLoS One
PMCID: 3632532
PMID: 23630569
DOI: 10.1371/journal.pone.0059737
call_split See protocol

[…] ed to comprehensively evaluate β atomic contacts.The first Bahadur dataset contains 178 crystal packing and 113 biological homodimers from the previous works , . This dataset has been used to develop DiMoVo .The second Ponstingl dataset has 95 crystal packing and 76 homodimers . This dataset has been used in several existing works , , including PITA and PISA .The third non-redundant dataset is co […]

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DiMoVo institution(s)
Department of Structural Biology, Fairchild Science Building, Stanford University School of Medicine, Stanford, CA, USA; Yeast Structural Genomics, IBBMC UMR 8619, Universite Paris-Sud, Orsay, France; LEBS UPR 9063, CNRS, Gif-sur-Yvette, France
DiMoVo funding source(s)
This work was supported by the Association pour la Recherche contre le Cancer (ARC).

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