HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Bosco K Ho, Franz Gruswitz

ABSTRACT

BACKGROUND: An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated. RESULTS: To cleanly visualize a channel surface, we present HOLLOW, a program that generates a "casting" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces. CONCLUSION: The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net. More... »

PAGES

49

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1472-6807-8-49

DOI

http://dx.doi.org/10.1186/1472-6807-8-49

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1017381549

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19014592


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/2008/0306", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Physical Chemistry (incl. Structural)", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/03", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Chemical Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computer Graphics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Structure", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Surface Properties", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of California, San Francisco", 
          "id": "https://www.grid.ac/institutes/grid.266102.1", 
          "name": [
            "Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, 94158-2517, San Francisco, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ho", 
        "givenName": "Bosco K", 
        "id": "sg:person.01300627767.31", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300627767.31"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, San Francisco", 
          "id": "https://www.grid.ac/institutes/grid.266102.1", 
          "name": [
            "Department of Biochemistry and Biophysics, Center for Structure of Membrane Proteins (CSMP), University of California, San Francisco, 94158-2517, San Francisco, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gruswitz", 
        "givenName": "Franz", 
        "id": "sg:person.01123046735.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123046735.29"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/s10969-008-9046-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004124679", 
          "https://doi.org/10.1007/s10969-008-9046-7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0263-7855(97)00009-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004510960"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.str.2007.10.007", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005766897"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.181342398", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006228920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(66)90088-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006330667"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(73)90011-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010215061"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0263-7855(95)00073-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017175175"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444993011333", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037190302"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0021889883010985", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041454136"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-316", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044949819", 
          "https://doi.org/10.1186/1471-2105-7-316"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2008-12", 
    "datePublishedReg": "2008-12-01", 
    "description": "BACKGROUND: An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated.\nRESULTS: To cleanly visualize a channel surface, we present HOLLOW, a program that generates a \"casting\" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces.\nCONCLUSION: The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1472-6807-8-49", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2440529", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2699220", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1028437", 
        "issn": [
          "2314-4343", 
          "1472-6807"
        ], 
        "name": "BMC Structural Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "8"
      }
    ], 
    "name": "HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures", 
    "pagination": "49", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "52cfd4f93fd681d36267b671749067d4fa6db8fd1028c11b480b098e8bd39131"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19014592"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101088689"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1472-6807-8-49"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1017381549"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1472-6807-8-49", 
      "https://app.dimensions.ai/details/publication/pub.1017381549"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T21:36", 
    "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_8687_00000511.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1472-6807-8-49"
  }
]
 

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.10.1186/1472-6807-8-49'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-8-49'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-8-49'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-8-49'


 

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

137 TRIPLES      21 PREDICATES      45 URIs      27 LITERALS      15 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1472-6807-8-49 schema:about N16ae089ce6224f8291be21c3b8f6d0ae
2 N46279c71f4cc421fac1082df05f6704a
3 N691db8725eee411182ff9a05216af02e
4 N9d248aeacd834114b07b9cb16230ab64
5 Nb65fd34a73464d0a9a55d0e77e1542c0
6 Nf4523c5e65954fce9c2562f5db57dc5c
7 anzsrc-for:03
8 anzsrc-for:0306
9 schema:author Nfdeaef9780be49aeb637aff66abd45d9
10 schema:citation sg:pub.10.1007/s10969-008-9046-7
11 sg:pub.10.1186/1471-2105-7-316
12 https://doi.org/10.1016/0022-2836(66)90088-x
13 https://doi.org/10.1016/0022-2836(73)90011-9
14 https://doi.org/10.1016/0263-7855(95)00073-9
15 https://doi.org/10.1016/j.str.2007.10.007
16 https://doi.org/10.1016/s0263-7855(97)00009-x
17 https://doi.org/10.1073/pnas.181342398
18 https://doi.org/10.1107/s0021889883010985
19 https://doi.org/10.1107/s0907444993011333
20 schema:datePublished 2008-12
21 schema:datePublishedReg 2008-12-01
22 schema:description BACKGROUND: An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated. RESULTS: To cleanly visualize a channel surface, we present HOLLOW, a program that generates a "casting" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces. CONCLUSION: The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net.
23 schema:genre research_article
24 schema:inLanguage en
25 schema:isAccessibleForFree true
26 schema:isPartOf N1de68ff918ff48f9a1f67b13d9ee24b5
27 N371530002cfe450e950deff7dce8b06a
28 sg:journal.1028437
29 schema:name HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
30 schema:pagination 49
31 schema:productId N300ab4d660a14ed18c43d0344dc9488c
32 N3df674e22ea84b57a7208982f5ccbc9c
33 N5193d8dc71d347e9bbeda84ae341798a
34 Nb7f544d476b144c38ca56873b67d743d
35 Nd8f7ebacb3d3495bacd487d5215d17b0
36 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017381549
37 https://doi.org/10.1186/1472-6807-8-49
38 schema:sdDatePublished 2019-04-10T21:36
39 schema:sdLicense https://scigraph.springernature.com/explorer/license/
40 schema:sdPublisher N5ef8bd781af44893b157cac590cf8cca
41 schema:url http://link.springer.com/10.1186%2F1472-6807-8-49
42 sgo:license sg:explorer/license/
43 sgo:sdDataset articles
44 rdf:type schema:ScholarlyArticle
45 N16ae089ce6224f8291be21c3b8f6d0ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
46 schema:name Protein Conformation
47 rdf:type schema:DefinedTerm
48 N1de68ff918ff48f9a1f67b13d9ee24b5 schema:issueNumber 1
49 rdf:type schema:PublicationIssue
50 N300ab4d660a14ed18c43d0344dc9488c schema:name pubmed_id
51 schema:value 19014592
52 rdf:type schema:PropertyValue
53 N371530002cfe450e950deff7dce8b06a schema:volumeNumber 8
54 rdf:type schema:PublicationVolume
55 N3df674e22ea84b57a7208982f5ccbc9c schema:name nlm_unique_id
56 schema:value 101088689
57 rdf:type schema:PropertyValue
58 N46279c71f4cc421fac1082df05f6704a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
59 schema:name Computer Graphics
60 rdf:type schema:DefinedTerm
61 N5193d8dc71d347e9bbeda84ae341798a schema:name doi
62 schema:value 10.1186/1472-6807-8-49
63 rdf:type schema:PropertyValue
64 N5ef8bd781af44893b157cac590cf8cca schema:name Springer Nature - SN SciGraph project
65 rdf:type schema:Organization
66 N691db8725eee411182ff9a05216af02e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
67 schema:name Surface Properties
68 rdf:type schema:DefinedTerm
69 N9d248aeacd834114b07b9cb16230ab64 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
70 schema:name Models, Molecular
71 rdf:type schema:DefinedTerm
72 Nb65fd34a73464d0a9a55d0e77e1542c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
73 schema:name Software
74 rdf:type schema:DefinedTerm
75 Nb7f544d476b144c38ca56873b67d743d schema:name readcube_id
76 schema:value 52cfd4f93fd681d36267b671749067d4fa6db8fd1028c11b480b098e8bd39131
77 rdf:type schema:PropertyValue
78 Nd8f7ebacb3d3495bacd487d5215d17b0 schema:name dimensions_id
79 schema:value pub.1017381549
80 rdf:type schema:PropertyValue
81 Ne0bb6e2a54b14a1da821cbcd70ee82b2 rdf:first sg:person.01123046735.29
82 rdf:rest rdf:nil
83 Nf4523c5e65954fce9c2562f5db57dc5c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Molecular Structure
85 rdf:type schema:DefinedTerm
86 Nfdeaef9780be49aeb637aff66abd45d9 rdf:first sg:person.01300627767.31
87 rdf:rest Ne0bb6e2a54b14a1da821cbcd70ee82b2
88 anzsrc-for:03 schema:inDefinedTermSet anzsrc-for:
89 schema:name Chemical Sciences
90 rdf:type schema:DefinedTerm
91 anzsrc-for:0306 schema:inDefinedTermSet anzsrc-for:
92 schema:name Physical Chemistry (incl. Structural)
93 rdf:type schema:DefinedTerm
94 sg:grant.2440529 http://pending.schema.org/fundedItem sg:pub.10.1186/1472-6807-8-49
95 rdf:type schema:MonetaryGrant
96 sg:grant.2699220 http://pending.schema.org/fundedItem sg:pub.10.1186/1472-6807-8-49
97 rdf:type schema:MonetaryGrant
98 sg:journal.1028437 schema:issn 1472-6807
99 2314-4343
100 schema:name BMC Structural Biology
101 rdf:type schema:Periodical
102 sg:person.01123046735.29 schema:affiliation https://www.grid.ac/institutes/grid.266102.1
103 schema:familyName Gruswitz
104 schema:givenName Franz
105 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123046735.29
106 rdf:type schema:Person
107 sg:person.01300627767.31 schema:affiliation https://www.grid.ac/institutes/grid.266102.1
108 schema:familyName Ho
109 schema:givenName Bosco K
110 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01300627767.31
111 rdf:type schema:Person
112 sg:pub.10.1007/s10969-008-9046-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004124679
113 https://doi.org/10.1007/s10969-008-9046-7
114 rdf:type schema:CreativeWork
115 sg:pub.10.1186/1471-2105-7-316 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044949819
116 https://doi.org/10.1186/1471-2105-7-316
117 rdf:type schema:CreativeWork
118 https://doi.org/10.1016/0022-2836(66)90088-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1006330667
119 rdf:type schema:CreativeWork
120 https://doi.org/10.1016/0022-2836(73)90011-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010215061
121 rdf:type schema:CreativeWork
122 https://doi.org/10.1016/0263-7855(95)00073-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017175175
123 rdf:type schema:CreativeWork
124 https://doi.org/10.1016/j.str.2007.10.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005766897
125 rdf:type schema:CreativeWork
126 https://doi.org/10.1016/s0263-7855(97)00009-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1004510960
127 rdf:type schema:CreativeWork
128 https://doi.org/10.1073/pnas.181342398 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006228920
129 rdf:type schema:CreativeWork
130 https://doi.org/10.1107/s0021889883010985 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041454136
131 rdf:type schema:CreativeWork
132 https://doi.org/10.1107/s0907444993011333 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037190302
133 rdf:type schema:CreativeWork
134 https://www.grid.ac/institutes/grid.266102.1 schema:alternateName University of California, San Francisco
135 schema:name Department of Biochemistry and Biophysics, Center for Structure of Membrane Proteins (CSMP), University of California, San Francisco, 94158-2517, San Francisco, CA, USA
136 Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, 94158-2517, San Francisco, CA, USA
137 rdf:type schema:Organization
 




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


...