Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, the...
Saved in:
| Published in | Bioinformatics Vol. 27; no. 6; pp. 785 - 790 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
15.03.2011
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1367-4811 1460-2059 |
| DOI | 10.1093/bioinformatics/btr009 |
Cover
| Abstract | Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.
Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.
Availability: CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.
Contact: taijiao@moon.ibp.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online. |
|---|---|
| AbstractList | Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling. Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy. We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling. CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html. Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.MOTIVATIONSide-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.RESULTSWe present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.AVAILABILITYCIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html. Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy. Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling. Availability: CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html. Contact: taijiao@moon.ibp.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online. |
| Author | Hu, Yun Jiang, Taijiao Miao, Zhichao Cao, Yang Song, Lin Tian, Liqing |
| Author_xml | – sequence: 1 givenname: Yang surname: Cao fullname: Cao, Yang – sequence: 2 givenname: Lin surname: Song fullname: Song, Lin – sequence: 3 givenname: Zhichao surname: Miao fullname: Miao, Zhichao – sequence: 4 givenname: Yun surname: Hu fullname: Hu, Yun – sequence: 5 givenname: Liqing surname: Tian fullname: Tian, Liqing – sequence: 6 givenname: Taijiao surname: Jiang fullname: Jiang, Taijiao |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23955843$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/21216772$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkUtP3DAUha0KVB7tT2jlTcUqxY7HdixWFSoPCYkNrKMb-5q4SuLBdmj5980wU6p2w-qexXfu6xyRvSlOSMgnzr5yZsRpF2KYfEwjlGDzaVcSY-YdOeRC6WrVcL73qpk4IEc5_2CMSSbVe3JQ85orretD0l-P6xSf0NEcHFa2hzDRMTocwvRAu2dq47x-0XaA3FcOC9oS4kQf5sXgaCiYlhWekGaEZHv6M5SeplhgxEQTDvALNvwHsu9hyPhxV4_J_cX3u_Or6ub28vr8201lhWalqlcdCFc3xjjvavBGesnQKaU4oOocdFY0xnpvpUIpG43eGmlB60YJJ6U4JifbvstZjzPm0o4hWxwGmDDOuW2Uadiq1uJtUiqtVKM3PT_vyLkb0bXrFEZIz-2fNy7Alx0A2cLgE0w25L-cMMuqq81IueVsijkn9K8IZ-0m1vbfWNttrIvv7D-fDeXlrSVBGN5w_wZjPLLi |
| CitedBy_id | crossref_primary_10_1007_s11704_024_40577_6 crossref_primary_10_1016_j_ibmb_2015_10_012 crossref_primary_10_1111_1346_8138_15045 crossref_primary_10_1021_acs_jcim_0c00951 crossref_primary_10_1021_acs_jcim_9b00812 crossref_primary_10_1021_acs_jctc_9b00309 crossref_primary_10_1007_s10493_021_00624_4 crossref_primary_10_1186_s12929_022_00845_8 crossref_primary_10_1038_s41431_024_01573_3 crossref_primary_10_1093_bioinformatics_btaa234 crossref_primary_10_1093_nar_gkw368 crossref_primary_10_1016_j_jbc_2022_102414 crossref_primary_10_1093_jisesa_iead073 crossref_primary_10_1074_jbc_RA119_011758 crossref_primary_10_1021_acs_jcim_1c00773 crossref_primary_10_1371_journal_pcbi_1008667 crossref_primary_10_1016_j_jmb_2024_168818 crossref_primary_10_1097_MD_0000000000014157 crossref_primary_10_1093_bib_bbw079 crossref_primary_10_1038_s41421_021_00256_3 crossref_primary_10_1186_s13578_022_00794_7 crossref_primary_10_1016_j_exppara_2013_10_003 crossref_primary_10_1038_s41598_017_14533_3 crossref_primary_10_1093_nar_gkac394 crossref_primary_10_1093_bioinformatics_btr538 crossref_primary_10_1093_jee_tou046 crossref_primary_10_1093_bib_bbab529 crossref_primary_10_1002_prot_25030 crossref_primary_10_1073_pnas_2216438120 crossref_primary_10_1038_s41598_024_61769_x crossref_primary_10_3390_bioengineering9080360 crossref_primary_10_1007_s10462_022_10350_x crossref_primary_10_1016_j_str_2024_03_015 crossref_primary_10_1093_bioinformatics_btr482 crossref_primary_10_1186_1471_2105_15_S12_S5 crossref_primary_10_1016_j_comptc_2022_113815 crossref_primary_10_3390_pathogens13080711 crossref_primary_10_1038_s41467_021_21853_6 crossref_primary_10_1093_bib_bbac330 crossref_primary_10_2139_ssrn_4049201 crossref_primary_10_1016_j_csbj_2019_12_007 crossref_primary_10_1016_j_jmb_2019_02_017 crossref_primary_10_1007_s00253_018_8998_1 crossref_primary_10_1021_acs_jcim_7b00679 crossref_primary_10_1016_j_ijbiomac_2016_03_043 crossref_primary_10_1016_j_ymeth_2018_01_015 |
| Cites_doi | 10.1110/ps.072855507 10.1093/protein/gzj001 10.1110/ps.041222905 10.1111/j.1399-3011.1979.tb01866.x 10.1186/1471-2105-11-306 10.1093/protein/8.4.363 10.1016/j.jmb.2007.11.033 10.1002/jcc.10420 10.1110/ps.062165906 10.1110/ps.03250104 10.1110/ps.062658307 10.1002/prot.21099 10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H 10.1111/j.1399-3011.1983.tb02062.x 10.1006/jmbi.1993.1100 10.1093/comjnl/7.2.149 10.1006/jmbi.1993.1170 10.1006/jmbi.1997.0926 10.1093/bioinformatics/bti144 10.1038/nsb0594-334 10.1016/S1359-0278(98)00050-9 10.1110/ps.03154503 10.1021/jp021564n 10.1002/prot.22570 10.1002/prot.22488 10.1002/pro.5560060807 10.1093/nar/28.1.235 10.1016/S0959-440X(02)00344-5 10.1002/(SICI)1097-0134(19981101)33:2<227::AID-PROT7>3.0.CO;2-F 10.1073/pnas.94.19.10172 10.1038/nsb0295-163 10.1038/356539a0 10.1016/0022-2836(76)90191-1 10.1016/0022-2836(78)90408-4 10.1007/11415770_32 10.1002/jcc.540040211 10.1002/prot.10131 10.1110/ps.24902 10.1006/jmbi.2001.4865 10.1021/ar010061h 10.1110/ps.035022.108 10.1111/j.1399-3011.1970.tb01679.x 10.1002/prot.10253 10.1016/0022-2836(87)90358-5 10.1016/S1359-0278(97)00006-0 |
| ContentType | Journal Article |
| Copyright | 2015 INIST-CNRS |
| Copyright_xml | – notice: 2015 INIST-CNRS |
| DBID | AAYXX CITATION IQODW CGR CUY CVF ECM EIF NPM 7X8 7QO 8FD FR3 P64 |
| DOI | 10.1093/bioinformatics/btr009 |
| DatabaseName | CrossRef Pascal-Francis Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic Biotechnology Research Abstracts Technology Research Database Engineering Research Database Biotechnology and BioEngineering Abstracts |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic Engineering Research Database Biotechnology Research Abstracts Technology Research Database Biotechnology and BioEngineering Abstracts |
| DatabaseTitleList | Engineering Research Database MEDLINE MEDLINE - Academic CrossRef |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1367-4811 1460-2059 |
| EndPage | 790 |
| ExternalDocumentID | 21216772 23955843 10_1093_bioinformatics_btr009 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GroupedDBID | --- -E4 -~X .2P .DC .I3 0R~ 1TH 23N 2WC 4.4 48X 53G 5GY 5WA 70D AAIJN AAIMJ AAJKP AAJQQ AAKPC AAMDB AAMVS AAOGV AAPQZ AAPXW AAUQX AAVAP AAVLN AAYXX ABEJV ABEUO ABGNP ABIXL ABNKS ABPQP ABPTD ABQLI ABWST ABXVV ABZBJ ACGFS ACIWK ACPRK ACUFI ACUXJ ACYTK ADBBV ADEYI ADEZT ADFTL ADGKP ADGZP ADHKW ADHZD ADMLS ADOCK ADPDF ADRDM ADRTK ADVEK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFZL AFGWE AFIYH AFOFC AFRAH AGINJ AGKEF AGQXC AGSYK AHMBA AHXPO AIJHB AJEEA AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC AMNDL APIBT APWMN ARIXL ASPBG AVWKF AXUDD AYOIW AZVOD BAWUL BAYMD BHONS BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE CITATION COF CS3 CZ4 DAKXR DIK DILTD DU5 D~K EBD EBS EE~ EJD EMOBN F5P F9B FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HW0 HZ~ IOX J21 JXSIZ KAQDR KOP KQ8 KSI KSN M-Z MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY NU- NVLIB O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED P2P PAFKI PEELM PQQKQ Q1. Q5Y R44 RD5 RNS ROL RPM RUSNO RW1 RXO SV3 TEORI TJP TLC TOX TR2 W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ~91 ~KM .-4 .GJ ABEFU ABNGD ACUKT AFFNX AGQPQ AI. AQDSO ATTQO AZFZN ELUNK HVGLF IQODW NTWIH O~Y PB- RIG RNI RZF RZO VH1 ZGI CGR CUY CVF ECM EIF NPM 7X8 482 7QO 8FD ABJNI FR3 P64 ROZ TN5 WH7 |
| ID | FETCH-LOGICAL-c370t-24ba3d2899dfd2af95f50ed6661ae6bdabc389cffc56e5587efc95ca77863d553 |
| ISSN | 1367-4803 1367-4811 |
| IngestDate | Tue Oct 07 09:12:21 EDT 2025 Fri Jul 11 08:43:46 EDT 2025 Mon Jul 21 05:48:38 EDT 2025 Mon Jul 21 09:17:24 EDT 2025 Tue Jul 01 03:27:03 EDT 2025 Thu Apr 24 23:07:14 EDT 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 6 |
| Keywords | Detection Modeling Side chain |
| Language | English |
| License | CC BY 4.0 |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c370t-24ba3d2899dfd2af95f50ed6661ae6bdabc389cffc56e5587efc95ca77863d553 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| PMID | 21216772 |
| PQID | 856766875 |
| PQPubID | 23479 |
| PageCount | 6 |
| ParticipantIDs | proquest_miscellaneous_869804273 proquest_miscellaneous_856766875 pubmed_primary_21216772 pascalfrancis_primary_23955843 crossref_primary_10_1093_bioinformatics_btr009 crossref_citationtrail_10_1093_bioinformatics_btr009 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2011-03-15 |
| PublicationDateYYYYMMDD | 2011-03-15 |
| PublicationDate_xml | – month: 03 year: 2011 text: 2011-03-15 day: 15 |
| PublicationDecade | 2010 |
| PublicationPlace | Oxford |
| PublicationPlace_xml | – name: Oxford – name: England |
| PublicationTitle | Bioinformatics |
| PublicationTitleAlternate | Bioinformatics |
| PublicationYear | 2011 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Krivov (2023012511544006400_B29) 2009; 77 Liang (2023012511544006400_B32) 2002; 11 Wang (2023012511544006400_B40) 2005; 14 Fiser (2023012511544006400_B19) 2002; 35 Berman (2023012511544006400_B2) 2000; 28 Hwang (2023012511544006400_B23) 1995; 8 Mendes (2023012511544006400_B36) 1999; 37 Chandras (2023012511544006400_B7) 1970; 2 Xiang (2023012511544006400_B43) 2007; 66 DeMaeyer (2023012511544006400_B10) 1997; 2 Dunbrack (2023012511544006400_B16) 1994; 1 Leach (2023012511544006400_B31) 1998; 33 Chothia (2023012511544006400_B8) 1976; 105 Bhat (2023012511544006400_B3) 1979; 13 Liu (2023012511544006400_B33) 2003; 50 Lu (2023012511544006400_B35) 2008; 17 Ponder (2023012511544006400_B39) 1987; 193 Harder (2023012511544006400_B21) 2010; 11 Canutescu (2023012511544006400_B6) 2003; 12 Desmet (2023012511544006400_B12) 2002; 48 Jain (2023012511544006400_B25) 2006; 15 Bower (2023012511544006400_B4) 1997; 267 Benedetti (2023012511544006400_B1) 1983; 22 Koehl (2023012511544006400_B28) 1995; 2 Peterson (2023012511544006400_B37) 2004; 13 Kingsford (2023012511544006400_B27) 2005; 21 Dunbrack (2023012511544006400_B15) 1993; 230 Feyfant (2023012511544006400_B18) 2007; 16 Krieger (2023012511544006400_B30) 2009; 77 Lu (2023012511544006400_B34) 2008; 376 Xiang (2023012511544006400_B42) 2001; 311 Zhang (2023012511544006400_B45) 2006; 19 Xu (2023012511544006400_B44) 2005; 3500 Brooks (2023012511544006400_B5) 1983; 4 Wilson (2023012511544006400_B41) 1993; 229 Dunbrack (2023012511544006400_B13) 2002; 12 Dahiyat (2023012511544006400_B9) 1997; 94 Desmet (2023012511544006400_B11) 1992; 356 Eyal (2023012511544006400_B17) 2004; 25 Jacobson (2023012511544006400_B24) 2002; 106 Janin (2023012511544006400_B26) 1978; 125 Fletcher (2023012511544006400_B20) 1964; 7 Dunbrack (2023012511544006400_B14) 1997; 6 Hartmann (2023012511544006400_B22) 2007; 16 Petrella (2023012511544006400_B38) 1998; 3 |
| References_xml | – volume: 16 start-page: 2030 year: 2007 ident: 2023012511544006400_B18 article-title: Modeling mutations in protein structures publication-title: Prot. Sci. doi: 10.1110/ps.072855507 – volume: 19 start-page: 55 year: 2006 ident: 2023012511544006400_B45 article-title: Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement publication-title: Prot. Eng. Des. Select. doi: 10.1093/protein/gzj001 – volume: 14 start-page: 1328 year: 2005 ident: 2023012511544006400_B40 article-title: Improved side-chain modeling for protein-protein docking publication-title: Prot. Sci. doi: 10.1110/ps.041222905 – volume: 13 start-page: 170 year: 1979 ident: 2023012511544006400_B3 article-title: Analysis of side-chain conformation in proteins publication-title: Int. J. Pept. Prot. Res. doi: 10.1111/j.1399-3011.1979.tb01866.x – volume: 11 start-page: 306 year: 2010 ident: 2023012511544006400_B21 article-title: Beyond rotamers: a generative, probabilistic model of side chains in proteins publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-306 – volume: 8 start-page: 363 year: 1995 ident: 2023012511544006400_B23 article-title: Side-chain prediction by neural networks and simulated annealing optimization publication-title: Prot. Eng. doi: 10.1093/protein/8.4.363 – volume: 376 start-page: 288 year: 2008 ident: 2023012511544006400_B34 article-title: OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2007.11.033 – volume: 25 start-page: 712 year: 2004 ident: 2023012511544006400_B17 article-title: Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins publication-title: J. Comput. Chem. doi: 10.1002/jcc.10420 – volume: 15 start-page: 2029 year: 2006 ident: 2023012511544006400_B25 article-title: Configurational-bias sampling technique for predicting side-chain conformations in proteins publication-title: Prot. Sci. doi: 10.1110/ps.062165906 – volume: 13 start-page: 735 year: 2004 ident: 2023012511544006400_B37 article-title: Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library publication-title: Prot. Sci. doi: 10.1110/ps.03250104 – volume: 16 start-page: 1294 year: 2007 ident: 2023012511544006400_B22 article-title: IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models publication-title: Prot. Sci. doi: 10.1110/ps.062658307 – volume: 66 start-page: 814 year: 2007 ident: 2023012511544006400_B43 article-title: Prediction of side-chain conformations on protein surfaces publication-title: Prot. Struct. Funct. Bioinform. doi: 10.1002/prot.21099 – volume: 37 start-page: 530 year: 1999 ident: 2023012511544006400_B36 article-title: Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model publication-title: Prot. Struct. Funct. Genet. doi: 10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H – volume: 22 start-page: 1 year: 1983 ident: 2023012511544006400_B1 article-title: Statistical and energetic analysis of side-chain conformations in oligopeptides publication-title: Int. J. Pep.t Prot. Res. doi: 10.1111/j.1399-3011.1983.tb02062.x – volume: 229 start-page: 996 year: 1993 ident: 2023012511544006400_B41 article-title: Modeling side-chain conformation for homologous proteins using an energy-based rotamer search publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1993.1100 – volume: 7 start-page: 149 year: 1964 ident: 2023012511544006400_B20 article-title: Function minimization by conjugate gradients publication-title: Comput J. doi: 10.1093/comjnl/7.2.149 – volume: 230 start-page: 543 year: 1993 ident: 2023012511544006400_B15 article-title: Backbone-dependent rotamer library for proteins - application to side-chain prediction publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1993.1170 – volume: 267 start-page: 1268 year: 1997 ident: 2023012511544006400_B4 article-title: Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1997.0926 – volume: 21 start-page: 1028 year: 2005 ident: 2023012511544006400_B27 article-title: Solving and analyzing side-chain positioning problems using linear and integer programming publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti144 – volume: 1 start-page: 334 year: 1994 ident: 2023012511544006400_B16 article-title: Conformational-analysis of the backbone-dependent rotamer preferences of protein side-chains publication-title: Nat. Struct. Biol. doi: 10.1038/nsb0594-334 – volume: 3 start-page: 353 year: 1998 ident: 2023012511544006400_B38 article-title: Protein sidechain conformer prediction: a test of the energy function publication-title: Fold. Des. doi: 10.1016/S1359-0278(98)00050-9 – volume: 12 start-page: 2001 year: 2003 ident: 2023012511544006400_B6 article-title: A graph-theory algorithm for rapid protein side-chain prediction publication-title: Prot. Sci. doi: 10.1110/ps.03154503 – volume: 106 start-page: 11673 year: 2002 ident: 2023012511544006400_B24 article-title: Force field validation using protein side chain prediction publication-title: J. Phys. Chem. B doi: 10.1021/jp021564n – volume: 77 start-page: 114 year: 2009 ident: 2023012511544006400_B30 article-title: Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8 publication-title: Prot. Struct. Funct. Bioinform. doi: 10.1002/prot.22570 – volume: 77 start-page: 778 year: 2009 ident: 2023012511544006400_B29 article-title: Improved prediction of protein side-chain conformations with SCWRL4 publication-title: Prot. Struct. Funct. Bioinform. doi: 10.1002/prot.22488 – volume: 6 start-page: 1661 year: 1997 ident: 2023012511544006400_B14 article-title: Bayesian statistical analysis of protein side-chain rotamer preferences publication-title: Prot. Sci. doi: 10.1002/pro.5560060807 – volume: 28 start-page: 235 year: 2000 ident: 2023012511544006400_B2 article-title: The Protein Data Bank publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.235 – volume: 12 start-page: 431 year: 2002 ident: 2023012511544006400_B13 article-title: Rotamer libraries in the 21(st) century publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(02)00344-5 – volume: 33 start-page: 227 year: 1998 ident: 2023012511544006400_B31 article-title: Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm publication-title: Prot. Struct. Funct. Genet. doi: 10.1002/(SICI)1097-0134(19981101)33:2<227::AID-PROT7>3.0.CO;2-F – volume: 94 start-page: 10172 year: 1997 ident: 2023012511544006400_B9 article-title: Probing the role of packing specificity in protein design publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.94.19.10172 – volume: 2 start-page: 163 year: 1995 ident: 2023012511544006400_B28 article-title: A self-consistent mean-field approach to simultaneous gap closure and side-chain positioning in homology modeling publication-title: Nat. Struct. Biol. doi: 10.1038/nsb0295-163 – volume: 356 start-page: 539 year: 1992 ident: 2023012511544006400_B11 article-title: The dead-end elimination theorem and its use in protein side-chain positioning publication-title: Nature doi: 10.1038/356539a0 – volume: 105 start-page: 1 year: 1976 ident: 2023012511544006400_B8 article-title: Nature of accessible and buried surfaces in proteins publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(76)90191-1 – volume: 125 start-page: 357 year: 1978 ident: 2023012511544006400_B26 article-title: Conformation of amino-acid side-chains in proteins publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(78)90408-4 – volume: 3500 start-page: 423 year: 2005 ident: 2023012511544006400_B44 article-title: Rapid protein side-chain packing via tree decomposition publication-title: Res. Comput. Mol. Biol., Lect Notes Comput Sci doi: 10.1007/11415770_32 – volume: 4 start-page: 187 year: 1983 ident: 2023012511544006400_B5 article-title: CHARMM: a program for macromolecular energy, minimization, and dynamics calculations publication-title: J. Comput. Chem. doi: 10.1002/jcc.540040211 – volume: 48 start-page: 31 year: 2002 ident: 2023012511544006400_B12 article-title: Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization publication-title: Prot. Struct. Funct. Genet. doi: 10.1002/prot.10131 – volume: 11 start-page: 322 year: 2002 ident: 2023012511544006400_B32 article-title: Side-chain modeling with an optimized scoring function publication-title: Prot. Sci. doi: 10.1110/ps.24902 – volume: 311 start-page: 421 year: 2001 ident: 2023012511544006400_B42 article-title: Extending the accuracy limits of prediction for side-chain conformations publication-title: J. Mol. Biol. doi: 10.1006/jmbi.2001.4865 – volume: 35 start-page: 413 year: 2002 ident: 2023012511544006400_B19 article-title: Evolution and physics in comparative protein structure modeling publication-title: Acc. Chem. Res. doi: 10.1021/ar010061h – volume: 17 start-page: 1576 year: 2008 ident: 2023012511544006400_B35 article-title: OPUS-Rota: a fast and accurate method for side-chain modeling publication-title: Prot. Sci. doi: 10.1110/ps.035022.108 – volume: 2 start-page: 223 year: 1970 ident: 2023012511544006400_B7 article-title: Studies on conformation of amino acids. 11. Analysis of observed side group conformations in proteins publication-title: Int. J. Prot. Res. doi: 10.1111/j.1399-3011.1970.tb01679.x – volume: 50 start-page: 49 year: 2003 ident: 2023012511544006400_B33 article-title: Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains publication-title: Prot. Struct. Funct. Genet. doi: 10.1002/prot.10253 – volume: 193 start-page: 775 year: 1987 ident: 2023012511544006400_B39 article-title: Tertiary templates for proteins - use of packing criteria in the enumeration of allowed sequences for different structural classes publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(87)90358-5 – volume: 2 start-page: 53 year: 1997 ident: 2023012511544006400_B10 article-title: All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination publication-title: Fold. Des. doi: 10.1016/S1359-0278(97)00006-0 |
| SSID | ssj0005056 ssj0051444 |
| Score | 2.2617366 |
| Snippet | Motivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the... Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation... |
| SourceID | proquest pubmed pascalfrancis crossref |
| SourceType | Aggregation Database Index Database Enrichment Source |
| StartPage | 785 |
| SubjectTerms | Algorithms Biological and medical sciences Computational Biology - methods Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Molecular Protein Conformation Proteins - chemistry Software |
| Title | Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/21216772 https://www.proquest.com/docview/856766875 https://www.proquest.com/docview/869804273 |
| Volume | 27 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: KQ8 dateStart: 19960101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVEBS databaseName: Inspec with Full Text customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: ADMLS dateStart: 19980101 isFulltext: true titleUrlDefault: https://www.ebsco.com/products/research-databases/inspec-full-text providerName: EBSCOhost – providerCode: PRVBFR databaseName: Free Medical Journals customDbUrl: eissn: 1367-4811 dateEnd: 20241103 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: DIK dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.freemedicaljournals.com providerName: Flying Publisher – providerCode: PRVFQY databaseName: GFMER Free Medical Journals customDbUrl: eissn: 1367-4811 dateEnd: 20241103 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: GX1 dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.gfmer.ch/Medical_journals/Free_medical.php providerName: Geneva Foundation for Medical Education and Research – providerCode: PRVAQN databaseName: PubMed Central customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: RPM dateStart: 20070101 isFulltext: true titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/ providerName: National Library of Medicine – providerCode: PRVOVD databaseName: Journals@Ovid LWW All Open Access Journal Collection Rolling customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: OVEED dateStart: 20010101 isFulltext: true titleUrlDefault: http://ovidsp.ovid.com/ providerName: Ovid – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1367-4811 dateEnd: 20220930 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwELagCAkJId4sj8oHxC2tEydOckRVqwpt28uutHCJbMdmV4LNsk0kyq9nnHGSDa8ClyixYiv2fLFnxuP5CHmdWmGNsSzIcimDuGRpoMJcBinPQwULBDfSGYpn5-J0Hr9bJIvBq9SeLqnVgf72y3Ml_yNVKAO5ulOy_yDZvlEogHuQL1xBwnD9KxmjRwBURse5GeglWPlIbePsf9ArddVs2nsNOvIyKE1tkBn8YwMV3KaB8Ym_vfOj9cpuq1p-Ntv2mMvXQXDdzu-q8slW651A-SPZulzfS78QOp-ND_adrnr8na3wtQ9LF6xfDZBq6zbrXRdE2MZg4SFMP2tylzw9YzhTGSyLBQNh-XTffqrFNAAeUrvzZoq8PX4JTpFB9KfZHTNfqVE_XUG9ZSwfFrRuE__8ojiZT6fF7Hgxe7P5EjiqMbcl73lXbpJbESwFju9jdrEY4oKYyy6ED6BNxkiL7DvYnQHL-eH4Mw7xI0bazd2NvIQfzSJDyu9NmFaVmd0n97wNQt8ioB6QG2b9kNxGVtKrR2TZwYoOsKIdrKi6oh2s6A-woggr2sOKIqyogxX1sKIDrB6T-cnx7Og08IQcgeYpq4MoVpKXzkQvbRlJmyc2YaYECziURqhSKg36r7ZWJ8IkSZYaq_NES5ejkJdJwp-QvXW1Ns8IFe4xlNwwyWILSqcGvTLjytpMMWOjCYm7gSy0z1bvSFM-FRg1wYvx-Bc4_hNy0FfbYLqW6yrsj6TU14p4Dj2I-YTQTmwFzLxuO02uTdVcFlkiUiHA3v_DKyLPHJkNtPIUJT60H0ahANP2-fWVX5A7w1_3kuzV28a8AlW4VvstdL8DGSLAnQ |
| linkProvider | Oxford University Press |
| 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=Improved+side-chain+modeling+by+coupling+clash-detection+guided+iterative+search+with+rotamer+relaxation&rft.jtitle=Bioinformatics&rft.au=Cao%2C+Yang&rft.au=Song%2C+Lin&rft.au=Miao%2C+Zhichao&rft.au=Hu%2C+Yun&rft.date=2011-03-15&rft.issn=1367-4803&rft.eissn=1460-2059&rft.volume=27&rft.issue=6&rft.spage=785&rft.epage=790&rft_id=info:doi/10.1093%2Fbioinformatics%2Fbtr009&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1367-4803&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1367-4803&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1367-4803&client=summon |