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Popular tool citations

chevron_left Pocket detection Protein-ligand docking Structure visualization Binding-site similarity detection Hydrogen atom site prediction chevron_right
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Protocols

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ProteinsPlus specifications

Information


Unique identifier OMICS_18277
Name ProteinsPlus
Interface Web user interface
Restrictions to use None
Input data A protein structure or a ligand structure.
Input format PDB, SDF
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • ActivityFinder
  • DoGSiteScorer
  • EDIA
  • HyPPI
  • METALizer
  • PoseView
  • Protoss
  • SIENA
  • StructureProfiler

Maintainers


  • person_outline Matthias Rarey <>
  • person_outline PoseView Team <>

Additional information


http://proteinsplus.zbh.uni-hamburg.de/help/index

Publications for ProteinsPlus

ProteinsPlus in pipeline

2015
PMCID: 4407318
PMID: 25888493
DOI: 10.1186/s12859-015-0563-7

[…] analysed through the structural similarity scores using probis tool (http://probis.cmm.ki.si/) [] by inspecting their physiochemical properties. active sites for both the proteins are determined by dogsitescorer [http://dogsite.zbh.uni-hamburg.de/] and probis tool. three dimensional structures of proteins were further used for structural topology alignment against non-redundant pdb (nr-pdb) […]


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ProteinsPlus in publications

 (33)
PMCID: 5896251
PMID: 29785196
DOI: 10.1155/2018/6813467

[…] entry, where ones with the highest confidence score (c-score) represented the best model []., the active sites in the evaluated tertiary structures of selected proteins were identified by using the dogsitescorer server [], in which the druggability of a pocket can be automatically predicted through the analyses of its size, shape, and chemical features. considering all descriptors, […]

PMCID: 5849182
PMID: 29560118
DOI: 10.18632/oncotarget.24132

[…] klk7 inhibitors are needed. in this experiment, we used computer aided drug screening to screen non-covalent inhibitors of klk7. firstly, we analyzed the crystal structure of klk7 (2qxh) using dogsitescorer server to identify the druggable region at the surface of the protein. the result showed that the most potent druggable regions were localized at the active site of klk7 including […]

PMCID: 5667448
PMID: 29118851
DOI: 10.1186/s13068-017-0944-4

[…] sugarcane bagasse was hydrated for 24 h prior analysis; a drop was directly applied to the sample pedestal and dried at room temperature for 12 h. after drying, samples were gold coated using a metalizer model med 020 (bal-tec, liechtenstein). images were obtained under vacuum. at least 10 images per sample were acquired from different areas to certify the reproducibility of the results., […]

PMCID: 5666896
PMID: 29065551
DOI: 10.3390/ijms18102217

[…] biology; bucurești, romania)., the three-dimensional structure file of the s. aureus srta was downloaded from the rcsb pdb database and was prepared by adding missing polar hydrogen atoms using the protoss tool provided by the proteins plus server []. all water molecules were removed and gasteiger charges were assigned to the protein structure. , the ligands’ chemical structures were retrieved […]

PMCID: 5648181
PMID: 29049350
DOI: 10.1371/journal.pone.0186401

[…] and authenticating putative pathogen targets [, ]. as mentioned above, for druggability analyses, the final list of essential non-host and host homologous protein targets were subjected to dogsitescorer in pdb format []. the dogsitescorer is an automated pocket detection and analysis tool for calculating the druggability of protein cavities. for each detected cavity the tool returns […]


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ProteinsPlus institution(s)
Universitat Hamburg, ZBH-Center for Bioinformatics, Hamburg, Germany; Institute of Physiology, Charite-Universitatsmedizin Berlin, Berlin, Germany
ProteinsPlus funding source(s)
Supported by de.NBI (in part) and German Federal Ministry of Education and Research [031L0105].

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