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WHAT IF specifications

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Unique identifier OMICS_32164
Name WHAT IF
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Windows
Programming languages Fortran
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for WHAT IF

WHAT IF citations

 (106)
library_books

Same but not alike: Structure, flexibility and energetics of domains in multi domain proteins are influenced by the presence of other domains

2018
PLoS Comput Biol
PMCID: 5825166
PMID: 29432415
DOI: 10.1371/journal.pcbi.1006008

[…] n method. Prior to energy minimization, the structures were repaired for missing residues and missing atoms. The missing residues were modelled using Rosetta 3.4 [] and missing atoms were built using WHAT IF 10.1a algorithm []. Normal modes were calculated by generating coarse-grained anisotropic network model (ANM) for proteins, with 15 Å as the cut-off for connecting the nodes. Distance-dependen […]

library_books

Identification and in silico structural analysis of Gallus gallus protein arginine methyltransferase 4 (PRMT4)

2017
FEBS Open Bio
PMCID: 5715347
PMID: 29226078
DOI: 10.1002/2211-5463.12323

[…] cale relaxation of the relative orientation, followed by a final short geometry minimization for bond lengths, bond angles, and planarity using Phenix 1.10.1‐2155 . The final model was evaluated with WHAT_IF version WHATCHECK 7.0 and PROCHECK v.3.5 . Ramachandran plot outliers were, where possible, manually corrected altering the dihedrals of the corresponding residues in Coot . The final Ramacha […]

library_books

Assessment of vocation of rifabutin and rifapentine in replace of rifampcin in drug resistance leprosy patients: a molecular simulation study

2017
PMCID: 5640893
PMID: 29071280
DOI: 10.22099/mbrc.2017.4084

[…] mical quality of the model and template. ERRAT tool [] was employed to uncover the overall quality factor of the protein. Standard bond lengths and bond angles of the rpoB model were elucidated using WHAT IF (http://swift.cmbi.ru.nl/whatif/) [] web server. ProSA tool [] was used in the refinement and validation of the modelled structure of rpoB to check the native protein folding energy of the mod […]

library_books

Genome scale detection of positive selection in nine primates predicts human virus evolutionary conflicts

2017
Nucleic Acids Res
PMCID: 5737536
PMID: 28977405
DOI: 10.1093/nar/gkx704

[…] in structures involving interactions between viral proteins and PSG. Optimized atomic-resolution structures were obtained from PDB_REDO (), visualized with YASARA (www.yasara.org), and analyzed using WHAT IF (). […]

library_books

Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

2017
PMCID: 5469174
PMID: 28616083
DOI: 10.1186/s13099-017-0184-y

[…] The MSA was used to develop an evolutionary model through EVA. The MSA and EVA analyses were performed as described [, ] using the YASARA/WHAT IF twinset [–]. EVA plots the entropy versus the variability to describe the variability pattern for every residue in the MSA. This plot contains five sectors that each holds residues with common […]

library_books

Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model

2017
Bioinformation
PMCID: 5498776
PMID: 28690376
DOI: 10.6026/97320630013122

[…] is used for making decision about its reliability. ERRAT showed an overall quality factor of 31.544, a result expected for crystallographic models with resolution>2.5A. Bfactor analysis is done with WHAT IF server reflected the mobility or flexibility of various parts of the molecule. Averaged B-factor deviation for protein backbone was 0.082 (Z score mean) and averaged standard deviation was 2.0 […]

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WHAT IF institution(s)
BIOSON Research Institute, Laboratory of Chemical Physics, Department of Chemistry, University of Groningen, Groningen, The Netherlands

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