CAVER: a new tool to explore routes from protein clefts, pockets and cavities View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-12

AUTHORS

Martin Petřek, Michal Otyepka, Pavel Banáš, Pavlína Košinová, Jaroslav Koča, Jiří Damborský

ABSTRACT

BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/. More... »

PAGES

316

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-7-316

DOI

http://dx.doi.org/10.1186/1471-2105-7-316

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1044949819

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16792811


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0801", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Artificial Intelligence and Image Processing", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computer Simulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Crystallography, X-Ray", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Internet", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Magnetic Resonance Spectroscopy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Structure, Secondary", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Proteomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Rhodococcus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Solvents", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sphingomonas", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Xanthobacter", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Masaryk University", 
          "id": "https://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pet\u0159ek", 
        "givenName": "Martin", 
        "id": "sg:person.01005556451.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01005556451.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Palack\u00fd University, Olomouc", 
          "id": "https://www.grid.ac/institutes/grid.10979.36", 
          "name": [
            "Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palack\u00fd University, t\u0159. Svobody 26, 771 46, Olomouc, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Otyepka", 
        "givenName": "Michal", 
        "id": "sg:person.01156750402.66", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156750402.66"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Palack\u00fd University, Olomouc", 
          "id": "https://www.grid.ac/institutes/grid.10979.36", 
          "name": [
            "Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palack\u00fd University, t\u0159. Svobody 26, 771 46, Olomouc, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ban\u00e1\u0161", 
        "givenName": "Pavel", 
        "id": "sg:person.0774406602.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774406602.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Palack\u00fd University, Olomouc", 
          "id": "https://www.grid.ac/institutes/grid.10979.36", 
          "name": [
            "Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palack\u00fd University, t\u0159. Svobody 26, 771 46, Olomouc, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ko\u0161inov\u00e1", 
        "givenName": "Pavl\u00edna", 
        "id": "sg:person.01270417665.87", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270417665.87"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Masaryk University", 
          "id": "https://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ko\u010da", 
        "givenName": "Jaroslav", 
        "id": "sg:person.01211201631.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01211201631.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Masaryk University", 
          "id": "https://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Damborsk\u00fd", 
        "givenName": "Ji\u0159\u00ed", 
        "id": "sg:person.01230502376.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01230502376.38"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1145/367766.368168", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000891687"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/235815.235821", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001929346"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1359-6446(04)03363-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002706320"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m306762200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009355818"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1110/ps3830102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011474914"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1110/ps3830102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011474914"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.1993.1436", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013865706"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti315", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016595832"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s090744499900534x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028257730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/1042091.1042117", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032564929"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444993011333", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037190302"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/363693a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037810409", 
          "https://doi.org/10.1038/363693a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/pro.5560070905", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040051084"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf01386390", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041716633", 
          "https://doi.org/10.1007/bf01386390"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/(sici)1097-0282(19991005)50:4<347::aid-bip1>3.0.co;2-r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049035249"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/etc.5620201205", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050148036"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/etc.5620201205", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050148036"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s010876738609983x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050706048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi00086a008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055160278"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi001539c", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055162882"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi001539c", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055162882"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi015734i", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055194920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi015734i", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055194920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi027280a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055196686"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi027280a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055196686"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi034748g", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055197390"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi034748g", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055197390"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi961151a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055212219"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi961151a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055212219"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9815187", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055216358"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9815187", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055216358"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi990849w", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055217839"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi990849w", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055217839"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9913855", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055218170"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi9913855", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055218170"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja0485715", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055837747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja0485715", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055837747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1090/qam/102435", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059346713"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/2945.942688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061146365"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/tmi.2002.806409", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061694336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1110/ps.ps3830102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061831289"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/j.1460-2075.1991.tb07647.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1078081422"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-12", 
    "datePublishedReg": "2006-12-01", 
    "description": "BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.\nRESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version.\nCONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-7-316", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.6891679", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6881747", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "7"
      }
    ], 
    "name": "CAVER: a new tool to explore routes from protein clefts, pockets and cavities", 
    "pagination": "316", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "d61c62da86350a16545e64176120e51d08da7857cbdc48da21cb8b06cc20754d"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "16792811"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-7-316"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1044949819"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-7-316", 
      "https://app.dimensions.ai/details/publication/pub.1044949819"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T13:14", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8659_00000507.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2105-7-316"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-316'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-316'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-316'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-7-316'


 

This table displays all metadata directly associated to this object as RDF triples.

262 TRIPLES      21 PREDICATES      74 URIs      35 LITERALS      23 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-7-316 schema:about N0524cfd8bbad4395a900297c0eca73fa
2 N27662f8670dd43b0bf9aedf2eaf2ebc9
3 N3ca316a977114e15a9a0fbcb61f90c84
4 N60d48b6aaa05427ba69b6cd411c782aa
5 N6b64753fa5a24e9695b139fbf67c3f26
6 N73fb40d726fd445d8870733a628b7d0b
7 N8763f4f1f47f43709c87277b7e0ef77e
8 N8ed0341a6c0f499585f68a6df4608aeb
9 N9e8c800fc37a45708f9665e567901aec
10 Nb5f4353781954299bb10314017d5783c
11 Nd4c27658c61e4660b53909d4a4c97e25
12 Nd7aed25fc5e946f385f8973b758eafad
13 Nf203d403461a40a2b174a002874bd0b0
14 Nf263d1cfff664cd5907a66458542d2f9
15 anzsrc-for:08
16 anzsrc-for:0801
17 schema:author Nc5b659a7206549538ab9b3301407889f
18 schema:citation sg:pub.10.1007/bf01386390
19 sg:pub.10.1038/363693a0
20 https://doi.org/10.1002/(sici)1097-0282(19991005)50:4<347::aid-bip1>3.0.co;2-r
21 https://doi.org/10.1002/etc.5620201205
22 https://doi.org/10.1002/j.1460-2075.1991.tb07647.x
23 https://doi.org/10.1002/pro.5560070905
24 https://doi.org/10.1006/jmbi.1993.1436
25 https://doi.org/10.1016/s1359-6446(04)03363-x
26 https://doi.org/10.1021/bi00086a008
27 https://doi.org/10.1021/bi001539c
28 https://doi.org/10.1021/bi015734i
29 https://doi.org/10.1021/bi027280a
30 https://doi.org/10.1021/bi034748g
31 https://doi.org/10.1021/bi961151a
32 https://doi.org/10.1021/bi9815187
33 https://doi.org/10.1021/bi990849w
34 https://doi.org/10.1021/bi9913855
35 https://doi.org/10.1021/ja0485715
36 https://doi.org/10.1074/jbc.m306762200
37 https://doi.org/10.1090/qam/102435
38 https://doi.org/10.1093/bioinformatics/bti315
39 https://doi.org/10.1107/s010876738609983x
40 https://doi.org/10.1107/s0907444993011333
41 https://doi.org/10.1107/s090744499900534x
42 https://doi.org/10.1109/2945.942688
43 https://doi.org/10.1109/tmi.2002.806409
44 https://doi.org/10.1110/ps.ps3830102
45 https://doi.org/10.1110/ps3830102
46 https://doi.org/10.1145/1042091.1042117
47 https://doi.org/10.1145/235815.235821
48 https://doi.org/10.1145/367766.368168
49 schema:datePublished 2006-12
50 schema:datePublishedReg 2006-12-01
51 schema:description BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.
52 schema:genre research_article
53 schema:inLanguage en
54 schema:isAccessibleForFree true
55 schema:isPartOf N30e20bf745c64c27bef7023c03a85150
56 Nb25e5439d09246e2bd1d34aec666488d
57 sg:journal.1023786
58 schema:name CAVER: a new tool to explore routes from protein clefts, pockets and cavities
59 schema:pagination 316
60 schema:productId N568f06e658914e45b8e78ee81e3ca099
61 N6e243f42b6e3425f85137e37b5adb1dd
62 N9b82e90a9e474c2dab880d2192aac44b
63 Na05cb4bf2fb64a69bb6937757d8522dc
64 Nf8c4767caa124b94a2b932bed5ec353d
65 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044949819
66 https://doi.org/10.1186/1471-2105-7-316
67 schema:sdDatePublished 2019-04-10T13:14
68 schema:sdLicense https://scigraph.springernature.com/explorer/license/
69 schema:sdPublisher N98af9f4423ce480abb4a0ff554a00017
70 schema:url http://link.springer.com/10.1186%2F1471-2105-7-316
71 sgo:license sg:explorer/license/
72 sgo:sdDataset articles
73 rdf:type schema:ScholarlyArticle
74 N0524cfd8bbad4395a900297c0eca73fa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Xanthobacter
76 rdf:type schema:DefinedTerm
77 N27662f8670dd43b0bf9aedf2eaf2ebc9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Proteomics
79 rdf:type schema:DefinedTerm
80 N30e20bf745c64c27bef7023c03a85150 schema:issueNumber 1
81 rdf:type schema:PublicationIssue
82 N3ca316a977114e15a9a0fbcb61f90c84 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Algorithms
84 rdf:type schema:DefinedTerm
85 N42efa72700824401a802399a58df01bc rdf:first sg:person.01230502376.38
86 rdf:rest rdf:nil
87 N568f06e658914e45b8e78ee81e3ca099 schema:name pubmed_id
88 schema:value 16792811
89 rdf:type schema:PropertyValue
90 N60d48b6aaa05427ba69b6cd411c782aa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Computer Simulation
92 rdf:type schema:DefinedTerm
93 N6a8ee3584dce4a9d9261f4fe3c763e98 rdf:first sg:person.01156750402.66
94 rdf:rest Ndf32d0b41d0e43b8bd074146d33b175c
95 N6b64753fa5a24e9695b139fbf67c3f26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
96 schema:name Solvents
97 rdf:type schema:DefinedTerm
98 N6e243f42b6e3425f85137e37b5adb1dd schema:name doi
99 schema:value 10.1186/1471-2105-7-316
100 rdf:type schema:PropertyValue
101 N73fb40d726fd445d8870733a628b7d0b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Protein Structure, Secondary
103 rdf:type schema:DefinedTerm
104 N8763f4f1f47f43709c87277b7e0ef77e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Rhodococcus
106 rdf:type schema:DefinedTerm
107 N8ed0341a6c0f499585f68a6df4608aeb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Proteins
109 rdf:type schema:DefinedTerm
110 N98af9f4423ce480abb4a0ff554a00017 schema:name Springer Nature - SN SciGraph project
111 rdf:type schema:Organization
112 N9b82e90a9e474c2dab880d2192aac44b schema:name dimensions_id
113 schema:value pub.1044949819
114 rdf:type schema:PropertyValue
115 N9e8c800fc37a45708f9665e567901aec schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Magnetic Resonance Spectroscopy
117 rdf:type schema:DefinedTerm
118 Na05cb4bf2fb64a69bb6937757d8522dc schema:name nlm_unique_id
119 schema:value 100965194
120 rdf:type schema:PropertyValue
121 Na927557ea5494ab8b8c144d48b980af9 rdf:first sg:person.01211201631.25
122 rdf:rest N42efa72700824401a802399a58df01bc
123 Nb17156640a3b471ca254bd9828d3af30 rdf:first sg:person.01270417665.87
124 rdf:rest Na927557ea5494ab8b8c144d48b980af9
125 Nb25e5439d09246e2bd1d34aec666488d schema:volumeNumber 7
126 rdf:type schema:PublicationVolume
127 Nb5f4353781954299bb10314017d5783c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Protein Conformation
129 rdf:type schema:DefinedTerm
130 Nc5b659a7206549538ab9b3301407889f rdf:first sg:person.01005556451.50
131 rdf:rest N6a8ee3584dce4a9d9261f4fe3c763e98
132 Nd4c27658c61e4660b53909d4a4c97e25 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Crystallography, X-Ray
134 rdf:type schema:DefinedTerm
135 Nd7aed25fc5e946f385f8973b758eafad schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Sphingomonas
137 rdf:type schema:DefinedTerm
138 Ndf32d0b41d0e43b8bd074146d33b175c rdf:first sg:person.0774406602.33
139 rdf:rest Nb17156640a3b471ca254bd9828d3af30
140 Nf203d403461a40a2b174a002874bd0b0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
141 schema:name Software
142 rdf:type schema:DefinedTerm
143 Nf263d1cfff664cd5907a66458542d2f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Internet
145 rdf:type schema:DefinedTerm
146 Nf8c4767caa124b94a2b932bed5ec353d schema:name readcube_id
147 schema:value d61c62da86350a16545e64176120e51d08da7857cbdc48da21cb8b06cc20754d
148 rdf:type schema:PropertyValue
149 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
150 schema:name Information and Computing Sciences
151 rdf:type schema:DefinedTerm
152 anzsrc-for:0801 schema:inDefinedTermSet anzsrc-for:
153 schema:name Artificial Intelligence and Image Processing
154 rdf:type schema:DefinedTerm
155 sg:grant.6881747 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2105-7-316
156 rdf:type schema:MonetaryGrant
157 sg:grant.6891679 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2105-7-316
158 rdf:type schema:MonetaryGrant
159 sg:journal.1023786 schema:issn 1471-2105
160 schema:name BMC Bioinformatics
161 rdf:type schema:Periodical
162 sg:person.01005556451.50 schema:affiliation https://www.grid.ac/institutes/grid.10267.32
163 schema:familyName Petřek
164 schema:givenName Martin
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01005556451.50
166 rdf:type schema:Person
167 sg:person.01156750402.66 schema:affiliation https://www.grid.ac/institutes/grid.10979.36
168 schema:familyName Otyepka
169 schema:givenName Michal
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01156750402.66
171 rdf:type schema:Person
172 sg:person.01211201631.25 schema:affiliation https://www.grid.ac/institutes/grid.10267.32
173 schema:familyName Koča
174 schema:givenName Jaroslav
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01211201631.25
176 rdf:type schema:Person
177 sg:person.01230502376.38 schema:affiliation https://www.grid.ac/institutes/grid.10267.32
178 schema:familyName Damborský
179 schema:givenName Jiří
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01230502376.38
181 rdf:type schema:Person
182 sg:person.01270417665.87 schema:affiliation https://www.grid.ac/institutes/grid.10979.36
183 schema:familyName Košinová
184 schema:givenName Pavlína
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01270417665.87
186 rdf:type schema:Person
187 sg:person.0774406602.33 schema:affiliation https://www.grid.ac/institutes/grid.10979.36
188 schema:familyName Banáš
189 schema:givenName Pavel
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774406602.33
191 rdf:type schema:Person
192 sg:pub.10.1007/bf01386390 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041716633
193 https://doi.org/10.1007/bf01386390
194 rdf:type schema:CreativeWork
195 sg:pub.10.1038/363693a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037810409
196 https://doi.org/10.1038/363693a0
197 rdf:type schema:CreativeWork
198 https://doi.org/10.1002/(sici)1097-0282(19991005)50:4<347::aid-bip1>3.0.co;2-r schema:sameAs https://app.dimensions.ai/details/publication/pub.1049035249
199 rdf:type schema:CreativeWork
200 https://doi.org/10.1002/etc.5620201205 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050148036
201 rdf:type schema:CreativeWork
202 https://doi.org/10.1002/j.1460-2075.1991.tb07647.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1078081422
203 rdf:type schema:CreativeWork
204 https://doi.org/10.1002/pro.5560070905 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040051084
205 rdf:type schema:CreativeWork
206 https://doi.org/10.1006/jmbi.1993.1436 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013865706
207 rdf:type schema:CreativeWork
208 https://doi.org/10.1016/s1359-6446(04)03363-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1002706320
209 rdf:type schema:CreativeWork
210 https://doi.org/10.1021/bi00086a008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055160278
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1021/bi001539c schema:sameAs https://app.dimensions.ai/details/publication/pub.1055162882
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1021/bi015734i schema:sameAs https://app.dimensions.ai/details/publication/pub.1055194920
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1021/bi027280a schema:sameAs https://app.dimensions.ai/details/publication/pub.1055196686
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1021/bi034748g schema:sameAs https://app.dimensions.ai/details/publication/pub.1055197390
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1021/bi961151a schema:sameAs https://app.dimensions.ai/details/publication/pub.1055212219
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1021/bi9815187 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055216358
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1021/bi990849w schema:sameAs https://app.dimensions.ai/details/publication/pub.1055217839
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1021/bi9913855 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055218170
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1021/ja0485715 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055837747
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1074/jbc.m306762200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009355818
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1090/qam/102435 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059346713
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1093/bioinformatics/bti315 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016595832
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1107/s010876738609983x schema:sameAs https://app.dimensions.ai/details/publication/pub.1050706048
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1107/s0907444993011333 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037190302
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1107/s090744499900534x schema:sameAs https://app.dimensions.ai/details/publication/pub.1028257730
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1109/2945.942688 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061146365
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1109/tmi.2002.806409 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061694336
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1110/ps.ps3830102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061831289
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1110/ps3830102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011474914
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1145/1042091.1042117 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032564929
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1145/235815.235821 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001929346
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1145/367766.368168 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000891687
255 rdf:type schema:CreativeWork
256 https://www.grid.ac/institutes/grid.10267.32 schema:alternateName Masaryk University
257 schema:name Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
258 National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
259 rdf:type schema:Organization
260 https://www.grid.ac/institutes/grid.10979.36 schema:alternateName Palacký University, Olomouc
261 schema:name Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacký University, tř. Svobody 26, 771 46, Olomouc, Czech Republic
262 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...