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Protocols

Situs specifications

Information


Unique identifier OMICS_26707
Name Situs
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0
Stability Stable
Registration required Yes
Maintained Yes

Subtool


  • DDforge

Versioning


No version available

Maintainer


  • person_outline Willy Wriggers

Publications for Situs

Situs citations

 (71)
library_books

Biophysical insights from a single chain camelid antibody directed against the Disrupted in Schizophrenia 1 protein

2018
PLoS One
PMCID: 5764400
PMID: 29324815
DOI: 10.1371/journal.pone.0191162

[…] ns obtained from DAMAVER were initially fit to the corresponding structural models using SUPCOMB, which takes care of the handedness ambiguity of the SAXS envelopes. After conversion of the latter to Situs-format volumetric maps, the relative positioning of the model structures was optimized by correlation-based refinement, as implemented in Sculptor []. […]

library_books

Two classes of protective antibodies against Pseudorabies virus variant glycoprotein B: Implications for vaccine design

2017
PLoS Pathog
PMCID: 5754140
PMID: 29261802
DOI: 10.1371/journal.ppat.1006777

[…] tted the crystal structure of PRV gB into the density map using CHIMERA [], which showed a high degree of matching. The atomic structure of 1H1 Fab was further fitted into the remaining density using SITUS [] with several rounds of orientation search. The special hinged structure of the Fab density allowed us to distinguish the relative orientation of heavy chain and light chain of Fab molecules d […]

library_books

High Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16

2017
Viruses
PMCID: 5744149
PMID: 29211035
DOI: 10.3390/v9120374

[…] 3J7E; U4 PDB ID 3J6R) and the constant domain of 3GK8 using Coot [,,]. Icosahedral symmetry was applied to the refined asymmetric unit model including Fabs to generate the capsid-Fab complex through Situs [,]. The capsid atomic model was then further refined iteratively using Phenix Real Space Refinement program []. At each iteration, the best model was visually inspected in Coot and adjusted man […]

call_split

Mechanism of formation of a toroid around DNA by the mismatch sensor protein

2017
Nucleic Acids Res
PMCID: 5758902
PMID: 29182773
DOI: 10.1093/nar/gkx1149
call_split See protocol

[…] ER (). For the docking of NgoSDNA:ADP in to the SAXS-derived model, the structure was modelled in Coot () using PDB 1E3M, followed by energy minimization in Discovery Studio Client 3.5 software tool. SITUS2.8.1 was used to fit the energy minimized homology model of NgoSDNA:ADP into the SAXS envelope derived from the averaged bead model (,). Figures were generated using VMD (). […]

call_split

At home at least: the taxonomic position of some north African Xerocrassa species (Pulmonata, )

2017
Zookeys
PMCID: 5674202
PMID: 29134034
DOI: 10.3897/zookeys.712.13066
call_split See protocol

[…] y using simple magnifying glasses. Preserved animals were dissected under LEICA M212 stereo-microscope using thin tweezers. The genital organs of the specimens were removed from the body, the genital situs (i.e. the outer morphology of the complete hermaphroditic genital organ) and further morphological details were investigated. After that, shells, genital situs, and details of the genital organs […]

library_books

Norovirus Escape from Broadly Neutralizing Antibodies Is Limited to Allostery Like Mechanisms

2017
PMCID: 5646240
PMID: 29062895
DOI: 10.1128/mSphere.00334-17

[…] The details of this loop are not as important as its general character. Most notably, CDR3 has an unusually high density of aromatics and hydrophobic residues (YYDYAVDYW).Using this crude model, the Situs package () was then used to model the Fab into the corresponding electron density of the 2D3/MNV complex. The variable domain from PIG was combined with the constant domains from our previous A6 […]

Citations

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Situs institution(s)
Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, USA
Situs funding source(s)
Supported in part by a grant from the National Institutes of Health (R01GM62968).

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