An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are...

Full description

Saved in:

Bibliographic Details
Published in:	BMC bioinformatics Vol. 16; no. 1; p. 23
Main Authors:	Cassioli, Andrea, Bardiaux, Benjamin, Bouvier, Guillaume, Mucherino, Antonio, Alves, Rafael, Liberti, Leo, Nilges, Michael, Lavor, Carlile, Malliavin, Thérèse E
Format:	Journal Article
Language:	English
Published:	London BioMed Central 28.01.2015 BioMed Central Ltd
Subjects:	Algorithms Analysis Biochemistry, Molecular Biology Bioinformatics Biomedical and Life Sciences Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer Simulation Humans Life Sciences Methodology Methodology Article Microarrays Models, Molecular Molecular biology Peptide Fragments - chemistry Protein Conformation Proteins - chemistry Molecular conformation Distance geometry Nuclear magnetic resonance Branch-and-prune algorithm Protein structure branch-and-prune algorithm Nuclear Magnetic Resonance 1 2
ISSN:	1471-2105, 1471-2105
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Abstract	Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm ( i BP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions We described the new algorithm i BP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm i BP has been applied on three α -helical peptides.
AbstractList	The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three [alpha]-helical peptides. Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three [alpha]-helical peptides. Keywords: Distance geometry, Branch-and-prune algorithm, Molecular conformation, Protein structure, Nuclear magnetic resonance The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.BACKGROUNDThe determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.RESULTSIn order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.CONCLUSIONSWe described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides. Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm ( i BP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions We described the new algorithm i BP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm i BP has been applied on three α -helical peptides. Background: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results: In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions: We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides. The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.
ArticleNumber	23
Audience	Academic
Author	Liberti, Leo Mucherino, Antonio Lavor, Carlile Cassioli, Andrea Alves, Rafael Bouvier, Guillaume Nilges, Michael Bardiaux, Benjamin Malliavin, Thérèse E
Author_xml	– sequence: 1 givenname: Andrea surname: Cassioli fullname: Cassioli, Andrea organization: LIX, Ecole Polytechnique – sequence: 2 givenname: Benjamin surname: Bardiaux fullname: Bardiaux, Benjamin organization: Institut Pasteur, Structural Bioinformatics Unit, CNRS UMR3528 – sequence: 3 givenname: Guillaume surname: Bouvier fullname: Bouvier, Guillaume organization: Institut Pasteur, Structural Bioinformatics Unit, CNRS UMR3528 – sequence: 4 givenname: Antonio surname: Mucherino fullname: Mucherino, Antonio organization: Université de Rennes-I – sequence: 5 givenname: Rafael surname: Alves fullname: Alves, Rafael organization: LIX, Ecole Polytechnique – sequence: 6 givenname: Leo surname: Liberti fullname: Liberti, Leo organization: LIX, Ecole Polytechnique, IBM TJ Watson Research Center – sequence: 7 givenname: Michael surname: Nilges fullname: Nilges, Michael organization: Institut Pasteur, Structural Bioinformatics Unit, CNRS UMR3528 – sequence: 8 givenname: Carlile surname: Lavor fullname: Lavor, Carlile organization: University of Campinas (IMECC-UNICAMP) – sequence: 9 givenname: Thérèse E surname: Malliavin fullname: Malliavin, Thérèse E email: therese.malliavin@pasteur.fr organization: Institut Pasteur, Structural Bioinformatics Unit, CNRS UMR3528
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/25627244$$D View this record in MEDLINE/PubMed https://pasteur.hal.science/pasteur-01120652$$DView record in HAL
BookMark	eNp9kktr3DAUhU1JaR7tD-imCLppFk51bcmyN4UhNE1goNDHWmjka4-CLU0leWj-feU6DZlQghYS0nfulY7OaXZkncUsewv0AqCuPgYoat7kFHhOGYccXmQnwATkBVB-9Gh9nJ2GcEspiJryV9lxwatCFIydZO3KEjX0zpu4HUl0BO00olcR0_ZAdi4EsxmQ7LyLaCzRznbOjyoaZwPZozfdnbE9USRgJK4jrQlRWY0zGaJXxsbwOnvZqSHgm_v5LPt59fnH5XW-_vrl5nK1zjWvIeZCVRvRYFltEMsWWmiY6JpWt02lO0V5URVKYc2obkS5wZqqitWi7YQqBYekOcs-LXV302bEVqNNFxjkzptR-TvplJGHJ9ZsZe_2kpU1KzlNBfKlwPaJ7Hq1ljsVIk5eUoCCVrzYQ-I_3Df07teEIcrRBI3DoCy6KUioBKvquqRNQt8vaK8GlCa5mG6gZ1yuOIOSi5qXibr4D5VGi6NJjmJn0v6B4PxAkJiIv2OvphDkzfdvh-y7x_Y8PPBfGhIAC6B9-neP3QMCVM6Jk0vikgVczomTswXiiUab-Dce8-cPzyqLRRlSF9ujl7du8jYF5BnRH6Ss6gE
CitedBy_id	crossref_primary_10_1038_s43588_022_00372_4 crossref_primary_10_1007_s00285_025_02203_2 crossref_primary_10_1007_s11590_018_1301_7 crossref_primary_10_1016_j_orl_2018_06_006 crossref_primary_10_1038_s41598_021_96370_z crossref_primary_10_1002_mma_4422 crossref_primary_10_1016_j_laa_2020_01_036 crossref_primary_10_1007_s00006_020_01085_5 crossref_primary_10_1016_j_eswa_2021_115993 crossref_primary_10_1007_s40314_021_01479_6 crossref_primary_10_1007_s10898_016_0493_6 crossref_primary_10_1007_s11128_022_03583_w crossref_primary_10_1007_s00006_018_0925_0 crossref_primary_10_1007_s10858_017_0108_7 crossref_primary_10_1002_jcc_26796 crossref_primary_10_1016_j_ins_2017_06_015 crossref_primary_10_1017_S1446181117000372 crossref_primary_10_1007_s10898_018_0635_0 crossref_primary_10_1089_cmb_2019_0013 crossref_primary_10_1007_s00006_016_0653_2 crossref_primary_10_1007_s00454_016_9846_7 crossref_primary_10_1007_s10288_016_0314_2 crossref_primary_10_1007_s10898_018_0610_9
Cites_doi	10.1126/science.7761829 10.1137/120875909 10.1021/ja061136l 10.1111/j.1475-3995.2007.00622.x 10.1074/jbc.M310328200 10.1007/s10898-010-9584-y 10.1007/s10589-011-9402-6 10.1089/cmb.2011.0173 10.1002/prot.10496 10.1002/prot.22980 10.1002/prot.22845 10.1007/s10898-013-0135-1 10.1002/bip.22132 10.1074/jbc.M114.571836 10.1089/cmb.2012.0089 10.1107/S0021889892009944 10.1007/s10858-009-9366-3 10.1093/bioinformatics/btu849 10.1007/978-3-642-56927-2 10.1002/jms.559 10.1016/j.sbi.2009.02.008 10.1016/j.dam.2013.01.020 10.1016/0022-2836(85)90134-2 10.1002/bip.360221211 10.1016/j.tcs.2005.09.062 10.1007/978-1-61779-480-3_22 10.1093/protein/2.1.27 10.1371/journal.pcbi.0020009 10.1002/prot.21091 10.1007/s11590-011-0302-6 10.1093/bioinformatics/bti144 10.1006/jmbi.1997.1284 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO;2-C 10.1080/152165401317291147 10.1073/pnas.1309842111 10.1023/A:1023221624213 10.1002/prot.24412 10.1093/bioinformatics/btl589 10.1517/17460441.2013.794780 10.1145/367766.368168 10.1007/s10858-009-9333-z 10.1137/1.9780898719604 10.1016/S0010-4655(01)00204-1 10.1021/ci400354b 10.1021/ja0319994 10.1002/pro.620 10.1002/jcc.10121 10.1007/s00006-015-0532-2 10.1007/s10898-011-9799-6 10.1073/pnas.1006142107 10.1110/ps.062427307 10.1107/S0108767391001071 10.1021/ja069004f 10.1146/annurev.biophys.29.1.291 10.1145/1529282.1529451 10.1021/jp010454y 10.21914/anziamj.v42i0.608
ContentType	Journal Article
Copyright	Cassioli et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated. COPYRIGHT 2015 BioMed Central Ltd. licence_http://creativecommons.org/publicdomain/zero Cassioli et al.; licensee BioMed Central. 2015
Copyright_xml	– notice: Cassioli et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated. – notice: COPYRIGHT 2015 BioMed Central Ltd. – notice: licence_http://creativecommons.org/publicdomain/zero – notice: Cassioli et al.; licensee BioMed Central. 2015
DBID	C6C AAYXX CITATION CGR CUY CVF ECM EIF NPM ISR 7X8 1XC VOOES 5PM
DOI	10.1186/s12859-015-0451-1
DatabaseName	Springer Nature OA Free Journals CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Gale In Context: Science MEDLINE - Academic Hyper Article en Ligne (HAL) Hyper Article en Ligne (HAL) (Open Access) PubMed Central (Full Participant titles)
DatabaseTitle	CrossRef 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	fulltext_linktorsrc
Discipline	Biology
EISSN	1471-2105
ExternalDocumentID	PMC4384350 oai:HAL:pasteur-01120652v1 A541357853 25627244 10_1186_s12859_015_0451_1
Genre	Research Support, Non-U.S. Gov't Journal Article
GroupedDBID	--- 0R~ 23N 2WC 4.4 53G 5VS 6J9 7X7 88E 8AO 8FE 8FG 8FH 8FI 8FJ AAFWJ AAJSJ AAKPC AASML ABDBF ABUWG ACGFO ACGFS ACIHN ACIWK ACPRK ACUHS ADBBV ADMLS ADRAZ ADUKV AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHBYD AHMBA AHSBF AHYZX ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIJS ARAPS AZQEC BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BGLVJ BHPHI BMC BPHCQ BVXVI C6C CCPQU CS3 DIK DU5 DWQXO E3Z EAD EAP EAS EBD EBLON EBS EJD EMB EMK EMOBN ESX F5P FYUFA GNUQQ GROUPED_DOAJ GX1 H13 HCIFZ HMCUK HYE IAO ICD IHR INH INR ISR ITC K6V K7- KQ8 LK8 M1P M48 M7P MK~ ML0 M~E O5R O5S OK1 OVT P2P P62 PGMZT PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PUEGO RBZ RNS ROL RPM RSV SBL SOJ SV3 TR2 TUS UKHRP W2D WOQ WOW XH6 XSB AAYXX AFFHD CITATION ALIPV CGR CUY CVF ECM EIF NPM 7X8 123 1XC 2VQ C1A IPNFZ RIG VOOES 5PM
ID	FETCH-LOGICAL-c581t-7a6b79e36bee3d1d1947f9dcd96cfa05262aae840c973be80a6487df7a3751ee3
IEDL.DBID	RSV
ISICitedReferencesCount	38
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000356848200001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1471-2105
IngestDate	Tue Nov 04 01:57:26 EST 2025 Thu Nov 27 06:39:40 EST 2025 Sun Nov 09 10:15:21 EST 2025 Tue Nov 11 11:02:35 EST 2025 Tue Nov 04 18:20:27 EST 2025 Thu Nov 13 16:40:18 EST 2025 Mon Jul 21 06:07:17 EDT 2025 Sat Nov 29 05:39:57 EST 2025 Tue Nov 18 22:35:12 EST 2025 Sat Sep 06 07:27:17 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	1
Keywords	Molecular conformation Distance geometry Nuclear magnetic resonance Branch-and-prune algorithm Protein structure branch-and-prune algorithm Nuclear Magnetic Resonance 1 2
Language	English
License	licence_http://creativecommons.org/publicdomain/zero/: http://creativecommons.org/publicdomain/zero This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c581t-7a6b79e36bee3d1d1947f9dcd96cfa05262aae840c973be80a6487df7a3751ee3
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ORCID	0000-0003-4014-9195 0000-0003-3139-6821 0000-0002-1451-8092
OpenAccessLink	https://link.springer.com/10.1186/s12859-015-0451-1
PMID	25627244
PQID	1674688309
PQPubID	23479
ParticipantIDs	pubmedcentral_primary_oai_pubmedcentral_nih_gov_4384350 hal_primary_oai_HAL_pasteur_01120652v1 proquest_miscellaneous_1674688309 gale_infotracmisc_A541357853 gale_infotracacademiconefile_A541357853 gale_incontextgauss_ISR_A541357853 pubmed_primary_25627244 crossref_primary_10_1186_s12859_015_0451_1 crossref_citationtrail_10_1186_s12859_015_0451_1 springer_journals_10_1186_s12859_015_0451_1
PublicationCentury	2000
PublicationDate	2015-01-28
PublicationDateYYYYMMDD	2015-01-28
PublicationDate_xml	– month: 01 year: 2015 text: 2015-01-28 day: 28
PublicationDecade	2010
PublicationPlace	London
PublicationPlace_xml	– name: London – name: England
PublicationTitle	BMC bioinformatics
PublicationTitleAbbrev	BMC Bioinformatics
PublicationTitleAlternate	BMC Bioinformatics
PublicationYear	2015
Publisher	BioMed Central BioMed Central Ltd
Publisher_xml	– name: BioMed Central – name: BioMed Central Ltd
References	H Fan (451_CR65) 2003; 53 P Güntert (451_CR31) 1997; 273 451_CR54 A Mucherino (451_CR34) 2011 J Lorieau (451_CR59) 2010; 107 I Coope (451_CR29) 2000; 42 S Potluri (451_CR12) 2006; 65 J Zeng (451_CR17) 2009; 45 L Liberti (451_CR55) 2014; 165 W Kabsch (451_CR40) 1983; 22 L Miri (451_CR62) 2014; 82 C Lavor (451_CR23) 2012; 52 A Grishaev (451_CR39) 2004; 126 451_CR48 Q Dong (451_CR35) 2003; 26 451_CR47 P Güntert (451_CR32) 2001; 138 C Wang (451_CR11) 1998; 32 L Liberti (451_CR49) 2008; 15 C Kingsford (451_CR19) 2005; 21 451_CR61 P Reardon (451_CR16) 2014; 111 J Martin (451_CR14) 2011; 18 R O’Neil (451_CR22) 2003; 278 A Sinz (451_CR3) 2003; 38 L Liberti (451_CR28) 2014; 165 H Brönnimann (451_CR46) 2006; 351 X Huang (451_CR1) 2014; 289 L Liberti (451_CR8) 2014; 56 B López-Méndez (451_CR33) 2006; 128 J Berg (451_CR30) 2006 M Bello (451_CR6) 2013; 8 D Gordon (451_CR18) 2003; 24 A Bernard (451_CR73) 2008; 79 W Rieping (451_CR68) 2007; 23 M Marti-Renom (451_CR4) 2000; 29 M Respondek (451_CR58) 2007; 129 L Wang (451_CR20) 2005 C Lavor (451_CR24) 2013; 56 P Guntert (451_CR69) 2004; 278 E Anderson (451_CR44) 1999 H Berman (451_CR57) 2013; 99 451_CR72 V Kanelis (451_CR2) 2001; 52 RA Engh (451_CR25) 1991; 47 L-Q Lee (451_CR45) 2002 V Costa (451_CR51) 2014; 60 G Bouvier (451_CR63) 2014; 54 K Lasker (451_CR71) 2010; 78 W Rocchia (451_CR26) 2001; 105 T Kohonen (451_CR64) 2001 Y Shen (451_CR38) 2009; 44 N Josuttis (451_CR43) 1999 J Martin (451_CR15) 2011; 20 L Liberti (451_CR53) 2013 G Crippen (451_CR7) 1988 M Nilges (451_CR9) 1988; 2 MH Austern (451_CR42) 1998 S Vajda (451_CR5) 2009; 19 C Lavor (451_CR52) 2012; 52 B Honig (451_CR27) 1995; 268 RW Floyd (451_CR37) 1962; 5 L Wang (451_CR21) 2006; 13 C Lavor (451_CR50) 2011; 50 R Laskowski (451_CR60) 1993; 26 D Abrahams (451_CR41) 2004 W Braun (451_CR67) 1985; 186 C Lavor (451_CR56) 2012; 6 S Nabuurs (451_CR66) 2006; 2 B Alipanahi (451_CR10) 2013; 20 P Guerry (451_CR70) 2012; 831 S Potluri (451_CR13) 2007; 16 451_CR36
References_xml	– volume: 268 start-page: 1144 issue: 5214 year: 1995 ident: 451_CR27 publication-title: Science doi: 10.1126/science.7761829 – volume: 56 start-page: 3 year: 2014 ident: 451_CR8 publication-title: SIAM Rev doi: 10.1137/120875909 – volume: 128 start-page: 13112 year: 2006 ident: 451_CR33 publication-title: J Am Chem Soc doi: 10.1021/ja061136l – volume: 15 start-page: 1 year: 2008 ident: 451_CR49 publication-title: Int Trans Operational Res doi: 10.1111/j.1475-3995.2007.00622.x – volume: 278 start-page: 52980 year: 2003 ident: 451_CR22 publication-title: J Biol Chem doi: 10.1074/jbc.M310328200 – volume: 50 start-page: 329 year: 2011 ident: 451_CR50 publication-title: J Global Optimization doi: 10.1007/s10898-010-9584-y – ident: 451_CR47 – volume: 52 start-page: 115 year: 2012 ident: 451_CR52 publication-title: Comput Optimization App doi: 10.1007/s10589-011-9402-6 – volume: 18 start-page: 1507 year: 2011 ident: 451_CR14 publication-title: J Comput Biol doi: 10.1089/cmb.2011.0173 – volume-title: Pardalos, P., Rebennack, S. (eds.) Lecture Notes in Computer Science 6630 year: 2011 ident: 451_CR34 – volume: 53 start-page: 111 year: 2003 ident: 451_CR65 publication-title: Proteins doi: 10.1002/prot.10496 – volume: 79 start-page: 1525 year: 2008 ident: 451_CR73 publication-title: Proteins doi: 10.1002/prot.22980 – volume: 78 start-page: 3205 year: 2010 ident: 451_CR71 publication-title: Proteins doi: 10.1002/prot.22845 – volume: 60 start-page: 333 year: 2014 ident: 451_CR51 publication-title: J Global Optimization doi: 10.1007/s10898-013-0135-1 – volume: 99 start-page: 218 year: 2013 ident: 451_CR57 publication-title: Biopolymers doi: 10.1002/bip.22132 – volume: 289 start-page: 17203 year: 2014 ident: 451_CR1 publication-title: J Biol Chem doi: 10.1074/jbc.M114.571836 – volume: 20 start-page: 296 year: 2013 ident: 451_CR10 publication-title: J Comput Biol doi: 10.1089/cmb.2012.0089 – volume: 26 start-page: 283 year: 1993 ident: 451_CR60 publication-title: J Appl Crystallogr doi: 10.1107/S0021889892009944 – volume: 45 start-page: 265 year: 2009 ident: 451_CR17 publication-title: J Biomol NMR doi: 10.1007/s10858-009-9366-3 – ident: 451_CR61 doi: 10.1093/bioinformatics/btu849 – volume-title: Generic Programming and the STL: Using and Extending the C++ Standard Template Library year: 1998 ident: 451_CR42 – volume: 278 start-page: 353 year: 2004 ident: 451_CR69 publication-title: Methods Mol Biol – volume-title: Self-organizing Maps year: 2001 ident: 451_CR64 doi: 10.1007/978-3-642-56927-2 – volume-title: Mucherino A, Lavor C, Liberti L, Maculan N (eds.) Distance Geometry: Theory, Methods, and Applications year: 2013 ident: 451_CR53 – volume: 38 start-page: 1225 year: 2003 ident: 451_CR3 publication-title: J Mass Spectrometry doi: 10.1002/jms.559 – volume: 19 start-page: 164 year: 2009 ident: 451_CR5 publication-title: Curr Opin Struct Biol doi: 10.1016/j.sbi.2009.02.008 – volume: 165 start-page: 213 year: 2014 ident: 451_CR28 publication-title: Discrete Appl Mathematics doi: 10.1016/j.dam.2013.01.020 – volume: 186 start-page: 611 year: 1985 ident: 451_CR67 publication-title: J Mol Biol doi: 10.1016/0022-2836(85)90134-2 – volume: 22 start-page: 2577 issue: 12 year: 1983 ident: 451_CR40 publication-title: Biopolymers doi: 10.1002/bip.360221211 – volume: 351 start-page: 111 issue: 1 year: 2006 ident: 451_CR46 publication-title: Theor Comput Sci doi: 10.1016/j.tcs.2005.09.062 – volume: 831 start-page: 429 year: 2012 ident: 451_CR70 publication-title: Methods Mol Biol doi: 10.1007/978-1-61779-480-3_22 – volume: 2 start-page: 27 year: 1988 ident: 451_CR9 publication-title: Protein Eng doi: 10.1093/protein/2.1.27 – volume: 2 start-page: 9 year: 2006 ident: 451_CR66 publication-title: PLoS Computional Biol doi: 10.1371/journal.pcbi.0020009 – volume: 65 start-page: 203 year: 2006 ident: 451_CR12 publication-title: Proteins doi: 10.1002/prot.21091 – volume-title: Biochemistry: International Edition year: 2006 ident: 451_CR30 – volume: 6 start-page: 783 year: 2012 ident: 451_CR56 publication-title: Optimization Lett doi: 10.1007/s11590-011-0302-6 – volume-title: The Boost Graph Library: User Guide and Reference Manual year: 2002 ident: 451_CR45 – volume-title: C++ Template Metaprogramming: Concepts, Tools, and Techniques from Boost and Beyond year: 2004 ident: 451_CR41 – volume: 21 start-page: 1028 year: 2005 ident: 451_CR19 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti144 – volume-title: An efficient and accurate algorithm for assigning nuclear Overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings. The IEEE computational systems bioinformatics conference (CSB) year: 2005 ident: 451_CR20 – volume: 273 start-page: 283 year: 1997 ident: 451_CR31 publication-title: J Mol Biol doi: 10.1006/jmbi.1997.1284 – volume: 32 start-page: 26 year: 1998 ident: 451_CR11 publication-title: Proteins doi: 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO;2-C – volume: 52 start-page: 291 year: 2001 ident: 451_CR2 publication-title: IUBMB Life doi: 10.1080/152165401317291147 – volume: 111 start-page: 1391 year: 2014 ident: 451_CR16 publication-title: Proc Nat Acad Sci USA doi: 10.1073/pnas.1309842111 – volume: 26 start-page: 321 issue: 3 year: 2003 ident: 451_CR35 publication-title: J Global Optimization doi: 10.1023/A:1023221624213 – volume: 82 start-page: 466 year: 2014 ident: 451_CR62 publication-title: Proteins doi: 10.1002/prot.24412 – volume: 23 start-page: 381 year: 2007 ident: 451_CR68 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl589 – volume: 52 start-page: 115 year: 2012 ident: 451_CR23 publication-title: Comput Optimization App doi: 10.1007/s10589-011-9402-6 – volume: 8 start-page: 821 year: 2013 ident: 451_CR6 publication-title: Expert Opin Drug Discovery doi: 10.1517/17460441.2013.794780 – volume: 5 start-page: 345 issue: 6 year: 1962 ident: 451_CR37 publication-title: Commun ACM doi: 10.1145/367766.368168 – volume: 44 start-page: 213 year: 2009 ident: 451_CR38 publication-title: J Biomol NMR doi: 10.1007/s10858-009-9333-z – volume-title: LAPACK Users’ Guide year: 1999 ident: 451_CR44 doi: 10.1137/1.9780898719604 – volume: 138 start-page: 155 year: 2001 ident: 451_CR32 publication-title: Comp Phys Commun doi: 10.1016/S0010-4655(01)00204-1 – volume: 54 start-page: 289 year: 2014 ident: 451_CR63 publication-title: J Chem Inf Model doi: 10.1021/ci400354b – volume: 126 start-page: 7281 issue: 23 year: 2004 ident: 451_CR39 publication-title: J Am Chem Soc doi: 10.1021/ja0319994 – volume: 20 start-page: 970 year: 2011 ident: 451_CR15 publication-title: Protein Sci doi: 10.1002/pro.620 – volume: 24 start-page: 232 year: 2003 ident: 451_CR18 publication-title: J Comput Chem doi: 10.1002/jcc.10121 – volume: 13 start-page: 1276 year: 2006 ident: 451_CR21 publication-title: J Comput Biol – ident: 451_CR48 – volume-title: Distance geometry and molecular conformation year: 1988 ident: 451_CR7 – ident: 451_CR72 doi: 10.1007/s00006-015-0532-2 – volume: 56 start-page: 855 year: 2013 ident: 451_CR24 publication-title: J Global Optimization doi: 10.1007/s10898-011-9799-6 – volume: 107 start-page: 11341 year: 2010 ident: 451_CR59 publication-title: Proc Nat Acad Sci USA doi: 10.1073/pnas.1006142107 – volume: 16 start-page: 69 year: 2007 ident: 451_CR13 publication-title: Protein Sci doi: 10.1110/ps.062427307 – volume: 47 start-page: 392 issue: 4 year: 1991 ident: 451_CR25 publication-title: Acta Crystallogr Sect A: Found Crystallogr doi: 10.1107/S0108767391001071 – volume: 129 start-page: 5228 year: 2007 ident: 451_CR58 publication-title: J Am Chem Soc doi: 10.1021/ja069004f – volume: 29 start-page: 291 year: 2000 ident: 451_CR4 publication-title: Annu Rev Biophys Biomol Struct doi: 10.1146/annurev.biophys.29.1.291 – volume-title: The C++ Standard Library: a Tutorial and Reference year: 1999 ident: 451_CR43 – ident: 451_CR36 doi: 10.1145/1529282.1529451 – volume: 105 start-page: 6507 issue: 28 year: 2001 ident: 451_CR26 publication-title: J Phys Chem B doi: 10.1021/jp010454y – volume: 42 start-page: 461 year: 2000 ident: 451_CR29 publication-title: ANZIAM Journal doi: 10.21914/anziamj.v42i0.608 – ident: 451_CR54 – volume: 165 start-page: 213 year: 2014 ident: 451_CR55 publication-title: Discrete Appl Mathematics doi: 10.1016/j.dam.2013.01.020
SSID	ssj0017805
Score	2.3686182
Snippet	Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common... The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently... Background The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common... Background: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common...
SourceID	pubmedcentral hal proquest gale pubmed crossref springer
SourceType	Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	23
SubjectTerms	Algorithms Analysis Biochemistry, Molecular Biology Bioinformatics Biomedical and Life Sciences Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer Simulation Humans Life Sciences Methodology Methodology Article Microarrays Models, Molecular Molecular biology Peptide Fragments - chemistry Protein Conformation Proteins - chemistry
Title	An algorithm to enumerate all possible protein conformations verifying a set of distance constraints
URI	https://link.springer.com/article/10.1186/s12859-015-0451-1 https://www.ncbi.nlm.nih.gov/pubmed/25627244 https://www.proquest.com/docview/1674688309 https://pasteur.hal.science/pasteur-01120652 https://pubmed.ncbi.nlm.nih.gov/PMC4384350
Volume	16
WOSCitedRecordID	wos000356848200001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVADU databaseName: Open Access: BioMedCentral Open Access Titles customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RBZ dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.biomedcentral.com/search/ providerName: BioMedCentral – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: DOA dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M~E dateStart: 20000101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Advanced Technologies & Aerospace Database (ProQuest) customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: P5Z dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/hightechjournals providerName: ProQuest – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M7P dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Computer Science Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: K7- dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/compscijour providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: 7X7 dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: BENPR dateStart: 20090101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: PIMPY dateStart: 20090101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVAVX databaseName: SpringerLINK Contemporary 1997-Present customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RSV dateStart: 20001201 isFulltext: true titleUrlDefault: https://link.springer.com/search?facet-content-type=%22Journal%22 providerName: Springer Nature
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwELfYBhIvfMMCozIIgQSKyKc_HgvatIlRRR1MhRfLSZy1UpdUdTqJ_547N60UBkjw4of4nFycO_sud_czIa-AOZHkTPiMSwwzBoGvq5T5UjBZRgI2CIeld37KRyMxmcisq-O2m2z3TUjSrdROrQV7b0PEWgPXN_URE8UHl2cPdjuB2jg-O9-GDhCkvwtf_nZYbwPqluGdKWZBXjcxr2dK_hIudbvQ0d3_4v8eudMZnXS4lpL75IapH5Bb62Mofzwk5bCmen7RLGft9JK2DcX0eARbNnB5ThcN6s3cUIfpMKspuNDbmkdLQRdmrliKampNS5uKlmiUgjQhpXWHULT2Efl6dPjl47Hfnb7gF6kIW59rlnNpYpYbE5dhGcqEV7IsSsmKSiNMTKS1Af-wkDzOjQg0A-enrLiOeRrCmMdkt25qs08ok4nIYZwJA5EUZZXjf6c8LCqwpbQsc48Em0-iig6aHJmbK-eiCKbWk6dg8hROngo98nY7ZLHG5fgb8Uv8zgrxLmpMqLnQK2vVydlYDVPYxRHwJ_bIm46oauDhhe7qE-AVECKrR3nQowSFLHrdr0Gctlwhfvfx8FQtNKjtaglshRHYfdEVsPViI3EK74HpbrVpVlZhaQgTIg6kR56sJXB7P7BRIw5GmUd4TzZ7D-z31LOpAw5PYgHWceCRdxsJVd2KZf88eU__ifoZuR05EQ_9SByQ3Xa5Ms_JzeKqndnlgOzwCXetGJC9D4ejbDxwf0Gg_cT9AWbeZtBm6Xfoz04-Z98GTrt_AkxuQso
linkProvider	Springer Nature
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9QwDI9ggMYL3x-FAQEhJoGq9TNNHk-I6SaOE9rGtLcoTdNdpaM9XXqT-O-x0_akMkCC18Zp3dSO7dr-hZC3wBxPcsZ9lglMMwaBr8qU-YIzUUQcDITD0jubZfM5Pz8XX_s-bjtUuw8pSbdTO7Xm7MCGiLUGoW_qIyaKDyHPjQQMFtbxHZ-cbVMHCNLfpy9_O21kgPpt-PoCqyCvuphXKyV_SZc6K3R497_4v0fu9E4nnXRScp9cM_UDcqs7hvLHQ1JMaqqWF826ahffadtQLI9HsGUDl5d01aDeLA11mA5VTSGE3vY8Wgq6ULlmKaqoNS1tSlqgUwrShJTWHULR2kfk2-Gn049Tvz99wdcpD1s_UyzPhIlZbkxchEUokqwUhS4E06VCmJhIKQPxoRZZnBseKAbBT1FmKs7SEOY8Jjt1U5unhDKR8BzmmTDgiS7KHP875aEuwZdSosg9EgyfROoemhyZW0oXonAmu8WTsHgSF0-GHnm_nbLqcDn-RvwGv7NEvIsaC2ou1MZaeXRyLCcpWHEE_Ik9st8TlQ08XKu-PwFeASGyRpR7I0pQSD0afgfitOUK8bunk5lcKVDbzRrYCiPw-6JLYOv1IHES74HlbrVpNlZiawjjPA6ER550Eri9H_ioUQZOmUeykWyOHjgeqauFAw5PYg7eceCRD4OEyn7Hsn9evGf_RP2K7E5Pv8zk7Gj--Tm5HTlxD_2I75Gddr0xL8hNfdlWdv3Sae1Pa0o82Q
linkToPdf	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3ra9RAEF-0avGL70e06ipiQQnNcx8fD_Vo8TiK1dJvyya76QWuyXGbK_jfO5PHQawK4tdkNjvZncnOZGZ-Q8hbYE4kGRM-4xLDjEHg6yJlvhRMmkjAAdFi6Z3O-Hwuzs7kcd_n1A3Z7kNIsqtpQJSmqjlYmaJTccEOXIi4a-AGpz7io_jg_txIsGcQuusnp9swAgL296HM3w4bHUb9J_n6AjMir5qbV7MmfwmdtifS9O5_v8s9cqc3Rumkk5775JqtHpBbXXvKHw-JmVRUL8_rddksLmhTU0ybRxBmC5eXdFWjPi0tbbEeyorCvNtaSEdBR8q2iIpq6mxD64IaNFZBypDStc0pGveIfJ9-_vbx0O-7Mvh5KsLG55plXNqYZdbGJjShTHghTW4kywuN8DGR1hb8xlzyOLMi0AycIlNwHfM0hDGPyU5VV_YpoUwmIoNxFrYuyU2R4f-oLMwLsLG0NJlHgmF7VN5DliNzS9W6LoKpbvEULJ7CxVOhR95vh6w6vI6_Eb_BPVeIg1Fhos253jinjk6-qkkKpzsCAcUe2e-Jihomz3VftwCvgNBZI8q9ESUoaj66_Q5Ea8sV4nofTmZqpUGdN2tgK4zAHowuga3Xg_QpfAamwVW23jiFJSNMiDiQHnnSSeP2eWC7RhyMNY_wkZyOJhzfqcpFCyiexAKs5sAjHwZpVf2XzP158Z79E_Ursnv8aapmR_Mvz8ntqJX20I_EHtlp1hv7gtzML5vSrV-2CvwTIjpFvQ
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=An+algorithm+to+enumerate+all+possible+protein+conformations+verifying+a+set+of+distance+constraints&rft.jtitle=BMC+bioinformatics&rft.au=Cassioli%2C+Andrea&rft.au=Bardiaux%2C+Benjamin&rft.au=Bouvier%2C+Guillaume&rft.au=Mucherino%2C+Antonio&rft.date=2015-01-28&rft.pub=BioMed+Central+Ltd&rft.issn=1471-2105&rft.eissn=1471-2105&rft.volume=16&rft_id=info:doi/10.1186%2Fs12859-015-0451-1&rft.externalDocID=A541357853
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1471-2105&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1471-2105&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1471-2105&client=summon