BALLDock/SLICK: a new method for protein-carbohydrate docking
Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle...
Uloženo v:
| Vydáno v: | Journal of chemical information and modeling Ročník 48; číslo 8; s. 1616 |
|---|---|
| Hlavní autoři: | , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
United States
01.08.2008
|
| Témata: | |
| ISSN: | 1549-9596 |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies. |
|---|---|
| AbstractList | Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies.Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies. Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies. |
| Author | Fuhrmann, Jan Kohlbacher, Oliver Kerzmann, Andreas Neumann, Dirk |
| Author_xml | – sequence: 1 givenname: Andreas surname: Kerzmann fullname: Kerzmann, Andreas organization: Division for Simulation of Biological Systems, Center for Bioinformatics, University of Tubingen, Sand 14, 72076 Tubingen, Germany – sequence: 2 givenname: Jan surname: Fuhrmann fullname: Fuhrmann, Jan – sequence: 3 givenname: Oliver surname: Kohlbacher fullname: Kohlbacher, Oliver – sequence: 4 givenname: Dirk surname: Neumann fullname: Neumann, Dirk |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/18646839$$D View this record in MEDLINE/PubMed |
| BookMark | eNo1jzlPw0AYRLcIIgcU_AG0FZ3J3uwiUQRzRViiIL21x7fEEHuDD6H8eywRqmnePM3M0aRJDSB0Qck1JYwufaUJoYQPEzSjUpjMSKOmaN51n4RwbhQ7RVOqlVCamxm6u18VxUPyX8v3Yp2_3mKLG_jBNfTbFHBMLd63qYeqybxtXdoeQmt7wGFsVM3HGTqJdtfB-TEXaPP0uMlfsuLteZ2viswKIfrMSX_DOLPaSgaMOOGojMYERR0nkWsRAwcCPERHpOaegpRCc4Bgg_HAFujqTztu-R6g68u66jzsdraBNHSlMkIxptUIXh7BwdUQyn1b1bY9lP9_2S-_6FVd |
| CitedBy_id | crossref_primary_10_3390_ijms21207702 crossref_primary_10_1016_j_sbi_2014_07_001 crossref_primary_10_1093_glycob_cwy102 crossref_primary_10_1208_s12248_012_9322_0 crossref_primary_10_1007_s10719_016_9745_4 crossref_primary_10_1016_j_jmgm_2016_10_018 crossref_primary_10_1016_j_carres_2014_10_028 crossref_primary_10_1016_j_drudis_2010_06_001 crossref_primary_10_1093_nar_gkp409 crossref_primary_10_1134_S1068162010040023 crossref_primary_10_3390_ijms23031451 crossref_primary_10_1016_j_jmgm_2019_04_001 crossref_primary_10_1093_bib_bbaa319 crossref_primary_10_1515_hsz_2021_0119 crossref_primary_10_1093_glycob_cwae068 crossref_primary_10_1007_s10822_009_9276_1 crossref_primary_10_1007_s00018_010_0352_4 crossref_primary_10_1007_s10822_011_9433_1 crossref_primary_10_1007_s11694_022_01567_z crossref_primary_10_1016_j_sbi_2010_07_005 crossref_primary_10_1093_glycob_cww055 crossref_primary_10_1093_glycob_cws147 crossref_primary_10_1016_j_drudis_2009_03_013 crossref_primary_10_1093_bib_bbab512 crossref_primary_10_1093_glycob_cwu102 crossref_primary_10_3762_bjoc_20_180 crossref_primary_10_1093_glycob_cwr059 crossref_primary_10_1016_j_carres_2020_108180 crossref_primary_10_1007_s10822_014_9794_3 crossref_primary_10_1517_17460440903186118 crossref_primary_10_3390_molecules22071038 |
| ContentType | Journal Article |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1021/ci800103u |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | no_fulltext_linktorsrc |
| Discipline | Chemistry |
| ExternalDocumentID | 18646839 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GroupedDBID | --- -~X 1WB 4.4 53G 55A 5GY 5VS 7~N AABXI ABJNI ABMVS ABQRX ABUCX ACGFS ACIWK ACNCT ACRPL ACS ADHLV ADNMO AEESW AENEX AEYZD AFEFF AHGAQ ALMA_UNASSIGNED_HOLDINGS ANPPW ANTXH AQSVZ CGR CUPRZ CUY CVF D0L DU5 EBS ECM ED~ EIF EJD F5P GGK GNL IH9 IHE JG~ LG6 NPM P2P PQQKQ RNS ROL UI2 VF5 VG9 W1F 7X8 ABBLG ABLBI |
| ID | FETCH-LOGICAL-a444t-b5c7232a8a52e20b4b15f99d61b30f384fd3e0e3dfb0583c1e55483eedad9ce2 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 48 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000258697400007&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1549-9596 |
| IngestDate | Thu Oct 02 06:35:49 EDT 2025 Wed Feb 19 01:42:42 EST 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 8 |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a444t-b5c7232a8a52e20b4b15f99d61b30f384fd3e0e3dfb0583c1e55483eedad9ce2 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| PMID | 18646839 |
| PQID | 69462286 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_69462286 pubmed_primary_18646839 |
| PublicationCentury | 2000 |
| PublicationDate | 2008-08-01 |
| PublicationDateYYYYMMDD | 2008-08-01 |
| PublicationDate_xml | – month: 08 year: 2008 text: 2008-08-01 day: 01 |
| PublicationDecade | 2000 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Journal of chemical information and modeling |
| PublicationTitleAlternate | J Chem Inf Model |
| PublicationYear | 2008 |
| SSID | ssj0033962 |
| Score | 2.1137562 |
| Snippet | Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes,... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 1616 |
| SubjectTerms | Algorithms Binding Sites Calibration Carbohydrate Metabolism Carbohydrates - chemistry Computational Biology - methods Dimerization Models, Molecular Protein Binding Protein Structure, Tertiary Proteins - chemistry Proteins - metabolism Software Design |
| Title | BALLDock/SLICK: a new method for protein-carbohydrate docking |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/18646839 https://www.proquest.com/docview/69462286 |
| Volume | 48 |
| WOSCitedRecordID | wos000258697400007&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1JS8NAGB2qFfTivtQ1B69Dk9lHFKnFohhLwSK9hcnMBIuQ1C6C_96ZpPEmHrzkNiT5ZnmP-b7vPQAuOSEWKWZgaKmGRIYZlBxl0Hd9ciNMZsoO79eY9_tiNJKDBriue2F8WWV9JpYHtSm0vyNvM0kYQoLdTj6g94zyudWlgcYKaGJHZPya5qOfHALGsrQT9RpkUFLJal0hFLX1WJQGB4vfeWWJL72t_33ZNthc8sqgUy2EHdCw-S5Y79Z2bnvg5q4Txw5S3tsv8WP36SpQgWPUQeUgHTjqGpSSDeMcajVNi7cv40UkAvd6f5m-D4a9-2H3AS69E6AihMxhSjV3ZEkJRZFFYUrSiGZSGhalOMywIJnBNrTYZGlIBdaRdbxCYIeYykht0QFYzYvcHoHA4T-1gqcOxxnRnAijdSp5KBEVkVWyBS7qsCTul3y-QeW2WMySOjAtcFhFNplUChpJJBhhjpod_zn2BGxUFRq-5O4UNDO3Ke0ZWNOf8_Fsel7OuHv2B8_fXzS1JQ |
| linkProvider | ProQuest |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=BALLDock%2FSLICK%3A+a+new+method+for+protein-carbohydrate+docking&rft.jtitle=Journal+of+chemical+information+and+modeling&rft.au=Kerzmann%2C+Andreas&rft.au=Fuhrmann%2C+Jan&rft.au=Kohlbacher%2C+Oliver&rft.au=Neumann%2C+Dirk&rft.date=2008-08-01&rft.issn=1549-9596&rft.volume=48&rft.issue=8&rft.spage=1616&rft_id=info:doi/10.1021%2Fci800103u&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1549-9596&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1549-9596&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1549-9596&client=summon |