StoneHinge protocols

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StoneHinge specifications


Unique identifier OMICS_09803
Name StoneHinge
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for StoneHinge

StoneHinge in pipeline

PMCID: 4028875
PMID: 24498948
DOI: 10.1186/1742-4933-10-43

[…] biologically important residues. the area and volume of clefts are significant for interacting residues, ligand binding, receptor binding etc. []. flexibility studies were based on the software stonehinge []. the implication of mutation on structure was studied using i-mutant 3.0 [], p-values for genotype associations were determined by chi2 test. risk factors were estimated by logistic […]

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StoneHinge in publications

PMCID: 5494296
PMID: 28680815
DOI: 10.1002/2211-5463.12243

[…] rpah rd+cd (pdb id: 2phm) to further analysis using the hingemaster software program that predicts the location of hinges in a protein by integrating existing hinge predictors (tlsmd, stonehinge, flexoracle and hingeseq) with a family of hinge predictors based on grouping residues with correlated normal mode motions . this truncated form was selected due to its higher resolution […]

PMCID: 4821432
PMID: 27081308
DOI: 10.4137/CIN.S38044

[…] hydrogen bonds (greater than 3.2 å)., besides, the native and mutant structures were subjected to simulated thermal denaturation through proflex, embedded in stone-hinge program available at describe the folding patterns. this web server simulated incremental thermal denaturation of the structure, as the calculated temperature rises, and hydrogen bonds weaker […]

PMCID: 4830698
PMID: 27123343
DOI: 10.1155/2016/4101059

[…] the hydrogen bonds begin to lose hold and break apart based on their distance, energy supplied, and their positions. msu proflex (formerly called first), a computational tool embedded in the program stonehinge, was used to identify rigid and flexible regions of known proteins. stonehingep and stonehinged modules incorporated in stonehinge program aided in the prediction of flexible hinge using […]

PMCID: 4522605
PMID: 26284089
DOI: 10.3389/fpls.2015.00567

[…] a stable dimeric structure. a hallmark of the dimerization core is a loop with a sequence motif g-s-x-p-a (motif d, figure ), which is predicted to be a hinge region according to both hingeprot and stonehinge softwares (; ). this loop contributes to the formation of the active site pocket together with residues from the motifs c and e. it also stabilizes the active site core by a hydrogen bond […]

PMCID: 3817810
PMID: 24564209
DOI: 10.1186/1471-2105-14-S18-S3

[…] proteins: bpti, 1bpi; ubiquitin, 1ubi; ci2, 2ci2; ribonuclease t1, 1bu4; cytochrome c, 1hrc; barnase, 1a2p; α-lactalbumin, 1hml; apo-myoglogin, 1a6m; interleukin-β, 1ilb; t4 lysozyme, 3lzm []. the stonehinge method and server for domain-level hinge prediction, developed in the gerstein lab, used the msu-first software as a module []. in their study they concluded that the msu-first-based […]

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StoneHinge institution(s)
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA

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