dDFIRE statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

dDFIRE specifications

Information


Unique identifier OMICS_07151
Name dDFIRE
Alternative name DFIRE2
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_07151
Name dDFIRE
Alternative name DFIRE2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://sparks-lab.org/pmwiki/download/index.php?Download=yueyang/DFIRE2-pair-src2.tgz
Maintained Yes

Download


download.png
download.png

Versioning


No version available

Publications for dDFIRE

dDFIRE citations

 (26)
library_books

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

2017
J Cheminform
PMCID: 5745212
PMID: 29282565
DOI: 10.1186/s13321-017-0254-7

[…] oses from the decoys was compared with those of two popular force field-based scoring functions used in protein–protein docking, ZRANK [] and FireDock [], and a knowledge-based scoring function named dDFIRE [].ZRANK is a force field-based scoring function that is a linear combination of atom-based potentials, including electrostatics, van der Waals, and desolvation potentials. Pairwise Atomic Cont […]

library_books

Diverse effects of distance cutoff and residue interval on the performance of distance dependent atom pair potential in protein structure prediction

2017
BMC Bioinformatics
PMCID: 5723101
PMID: 29221443
DOI: 10.1186/s12859-017-1983-3

[…] law. Many distance-dependent atom-pair potentials have been developed and widely used during the last two decades, such as RAPDF [], KBP [], Dfire [], Dope [], RW [] and so on. Some potentials (e.g. dDFIRE [], RWplus [], GOAP [], ROTAS []) also combine other energy terms for characterizing side-chain orientation, angle distribution, solvent accessibility or secondary structure preference, but the […]

library_books

Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments

2017
Proteins
PMCID: 5836938
PMID: 29178285
DOI: 10.1002/prot.25432

[…] fragment pairs randomly, maintaining corresponding pairs. We built and evaluated 3D‐models based on those alignments generated by shifting the fragment pairs. We submitted a 3D‐model with the highest dDFIRE score among models based on 300 alignments. We constructed quaternary structure models and then verified them in the same way as standard procedure. As a result, we were able to submit the mode […]

library_books

Structure based cross docking analysis of antibody–antigen interactions

2017
Sci Rep
PMCID: 5557897
PMID: 28811664
DOI: 10.1038/s41598-017-08414-y

[…] exes for both local refine and local dock routines (Fig. ). We also calculated the ROC curves for the complexes using four other widely-used scoring potentials computed using the CCharPPI web server: DFIRE2 interaction energy, total FireDock energy (antibody–antigen energy function), OPUS-PSP all-atom potential, and ZRANK2 scoring function. We considered the native cognate antibody–antigen interac […]

library_books

Heterologous expression of abaecin peptide from Apis mellifera in Pichia pastoris

2017
Microb Cell Fact
PMCID: 5414229
PMID: 28468662
DOI: 10.1186/s12934-017-0689-6

[…] software [], specifically the protocol of the AbinitioRelax software [–] was used to this goal. Approximately 2000 models were generated, one being selected after evaluation and validation using the dDFIRE []. The dDFIRE generates a score based on the free energy of the structure, therefore we select, among the thousands of models, one who has minor free energy. The peptide was visualized using t […]

call_split

ProQ3: Improved model quality assessments using Rosetta energy terms

2016
Sci Rep
PMCID: 5048106
PMID: 27698390
DOI: 10.1038/srep33509
call_split See protocol

[…] In this section, we compare the newly developed methods ProQRosFA, ProQRosCen and ProQ3 with their predecessor ProQ2 and other publicly available single-model methods: QMEAN, Qprob, SMOQ, DOPE, dDFIRE on the CASP11 and CAMEO data sets (see Methods). We compare the method performance in three categories: local (residue) level correlations, global (protein) level correlations and model selecti […]

Citations

Looking to check out a full list of citations?

dDFIRE institution(s)
Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana, USA

dDFIRE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review dDFIRE