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Associated diseases

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jsPISA specifications

Information


Unique identifier OMICS_08699
Name jsPISA
Interface Web user interface
Restrictions to use None
Input data PDB ID code, PDB-formatted file (also gzipped), PDBx (or mmCIF) -formatted file (also gzipped)
Programming languages Javascript
Computer skills Basic
Version 2.0.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Eugene Krissinel <>

Publications for jsPISA

jsPISA in publications

 (5)
PMCID: 5947778
PMID: 29533240
DOI: 10.1107/S2059798317014565

[…] 2013) and shelx (sheldrick, 2015)], mr with ab initio modelling (ample), a space-group validation pipeline (zanuda; lebedev & isupov, 2014) and crystal-packing and oligomerization analysis (jspisa; krissinel, 2015). in routine cases (no crystal pathologies, complete and good resolution data, correct sequence and a highly similar structural homologue), mr pipelines will find correct […]

PMCID: 5734687
PMID: 29253024
DOI: 10.1371/journal.pone.0189964

[…] are most usually as fab fragments and/or in complex with antigens rather than as unliganded scfv making a molecular level explanation problematic. visual examination of the structures as well as jspisa (protein interfaces, surfaces and assemblies—software) [,] analysis of the vl-vh domain interfaces revealed no common features that natalizumab and trastuzumab share which the others do not. […]

PMCID: 5660230
PMID: 29079741
DOI: 10.1038/s41598-017-14731-z

[…] a central role in the formation and stability of protein complexes. during the simulation, all the hydrogen bonds and the salt bridges which were present in the crystal structure (obtained from the jspisa server) were traced. the average number of hydrogen bonds calculated with a cut-off value of 3.2 å using the h-bond utility in gromacs is given in the fig. . it was observed […]

PMCID: 5537660
PMID: 28665339
DOI: 10.3390/v9070168

[…] prepared with pymol [] or chimera []. structure comparisons were done with dali [], oligomerization parameters (accessible and buried surfaces, estimated dissociation energies) were analyzed with jspisa [] and local three-fold axes were identified with symd []. multiple amino acid sequences were aligned by clustal w []., crystals belonging to two different space groups (p21 and r32) […]

PMCID: 5414403
PMID: 28512576
DOI: 10.1107/S2052252517005115

[…] that no single metric of interfaces can partition physiologically relevant interactions from mere crystal contacts (jones & thornton, 1996), so that current state-of-the-art approaches such as jspisa offer multiple relevant measurements such as interface area, hydrophobicity and predicted binding energy (krissinel, 2015). contact predictions offer a further appealing way to distinguish […]


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jsPISA institution(s)
CCP4, Research Complex at Harwell, Didcot, UK
jsPISA funding source(s)
Science and Technology Facilities Council UK

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