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Number Cited by Other Article(s)
1
Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024;187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
2
Coqueiro A, Fernandes DC, Danuello A, Regasini LO, Cardoso-Lopes EM, Young MCM, Brandão Torres LM, Campos VP, Silva DHS, da Silva Bolzani V, de Oliveira DF. Nematostatic activity of isoprenylated guanidine alkaloids from Pterogyne nitens and their interaction with acetylcholinesterase. Exp Parasitol 2023;250:108542. [PMID: 37178971 DOI: 10.1016/j.exppara.2023.108542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
3
López-Blanco JR, Dehouck Y, Bastolla U, Chacón P. Local Normal Mode Analysis for Fast Loop Conformational Sampling. J Chem Inf Model 2022;62:4561-4568. [PMID: 36099639 PMCID: PMC9516680 DOI: 10.1021/acs.jcim.2c00870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
4
Montiel-Garcia D, Rojas-Labra O, Santoyo-Rivera N, Reddy VS. Epitope-Analyzer: A structure-based webtool to analyze broadly neutralizing epitopes. J Struct Biol 2022;214:107839. [PMID: 35134530 PMCID: PMC8829422 DOI: 10.1016/j.jsb.2022.107839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 11/23/2022]
5
Kadukova M, Machado KDS, Chacón P, Grudinin S. KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. Bioinformatics 2021;37:943-950. [PMID: 32840574 DOI: 10.1093/bioinformatics/btaa748] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/27/2020] [Accepted: 08/18/2020] [Indexed: 11/12/2022]  Open
6
Zhao Z, Bourne PE. Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery. J Proteome Res 2020;19:4698-4705. [PMID: 32946692 PMCID: PMC7640976 DOI: 10.1021/acs.jproteome.0c00623] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 01/18/2023]
7
Simsir M, Broutin I, Mus-Veteau I, Cazals F. Studying dynamics without explicit dynamics: A structure-based study of the export mechanism by AcrB. Proteins 2020;89:259-275. [PMID: 32960482 DOI: 10.1002/prot.26012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/25/2020] [Accepted: 09/13/2020] [Indexed: 12/14/2022]
8
Wen Z, He J, Huang SY. Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinformatics 2020;36:478-486. [PMID: 31384919 DOI: 10.1093/bioinformatics/btz609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/22/2019] [Accepted: 08/02/2019] [Indexed: 12/12/2022]  Open
9
Carpentier M, Chomilier J. Protein multiple alignments: sequence-based versus structure-based programs. Bioinformatics 2020;35:3970-3980. [PMID: 30942864 DOI: 10.1093/bioinformatics/btz236] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 11/14/2022]  Open
10
Andreani J, Quignot C, Guerois R. Structural prediction of protein interactions and docking using conservation and coevolution. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
11
John A, Vetrivel U, Sivashanmugam M, Natarajan SK. Microsecond Simulation of the Proteoglycan-like Region of Carbonic Anhydrase IX and Design of Chemical Inhibitors Targeting pH Homeostasis in Cancer Cells. ACS OMEGA 2020;5:4270-4281. [PMID: 32149257 PMCID: PMC7057697 DOI: 10.1021/acsomega.9b04203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/08/2020] [Indexed: 05/09/2023]
12
Geometric description of self-interaction potential in symmetric protein complexes. Sci Data 2019;6:64. [PMID: 31101822 PMCID: PMC6525250 DOI: 10.1038/s41597-019-0058-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/29/2019] [Indexed: 01/23/2023]  Open
13
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. Genes (Basel) 2019;10:genes10030206. [PMID: 30857266 PMCID: PMC6470857 DOI: 10.3390/genes10030206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/03/2022]  Open
14
Pagès G, Charmettant B, Grudinin S. Protein model quality assessment using 3D oriented convolutional neural networks. Bioinformatics 2019;35:3313-3319. [DOI: 10.1093/bioinformatics/btz122] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/17/2019] [Accepted: 02/13/2019] [Indexed: 11/13/2022]  Open
15
Cazals F, Tetley R. Characterizing molecular flexibility by combining least root mean square deviation measures. Proteins 2019;87:380-389. [DOI: 10.1002/prot.25658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/20/2018] [Accepted: 01/09/2019] [Indexed: 12/29/2022]
16
Krieger C, Roselli S, Kellner-Thielmann S, Galati G, Schneider B, Grosjean J, Olry A, Ritchie D, Matern U, Bourgaud F, Hehn A. The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants. FRONTIERS IN PLANT SCIENCE 2018;9:820. [PMID: 29971079 PMCID: PMC6018538 DOI: 10.3389/fpls.2018.00820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/28/2018] [Indexed: 05/19/2023]
17
Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018;1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
18
Classification and Exploration of 3D Protein Domain Interactions Using Kbdock. Methods Mol Biol 2017. [PMID: 27115629 DOI: 10.1007/978-1-4939-3572-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
19
PDB-wide identification of biological assemblies from conserved quaternary structure geometry. Nat Methods 2017;15:67-72. [DOI: 10.1038/nmeth.4510] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023]
20
Fotoohifiroozabadi S, Mohamad MS, Deris S. Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions. J Bioinform Comput Biol 2017;15:1750004. [PMID: 28274174 DOI: 10.1142/s0219720017500044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
21
Roselli S, Olry A, Vautrin S, Coriton O, Ritchie D, Galati G, Navrot N, Krieger C, Vialart G, Bergès H, Bourgaud F, Hehn A. A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017;89:1119-1132. [PMID: 27943460 DOI: 10.1111/tpj.13450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 05/06/2023]
22
El Houasli M, Maigret B, Devignes MD, Ghoorah AW, Grudinin S, Ritchie DW. Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models. Proteins 2016;85:463-469. [PMID: 27701764 DOI: 10.1002/prot.25182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/13/2016] [Accepted: 09/24/2016] [Indexed: 11/06/2022]
23
Ritchie DW. Calculating and scoring high quality multiple flexible protein structure alignments. Bioinformatics 2016;32:2650-8. [PMID: 27187202 DOI: 10.1093/bioinformatics/btw300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 05/07/2016] [Indexed: 11/14/2022]  Open
24
Maghawry HA, Mostafa MGM, Gharib TF. A new protein structure representation for efficient protein function prediction. J Comput Biol 2015;21:936-46. [PMID: 25343279 DOI: 10.1089/cmb.2014.0137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
25
Aronchik I, Kundu A, Quirit JG, Firestone GL. The antiproliferative response of indole-3-carbinol in human melanoma cells is triggered by an interaction with NEDD4-1 and disruption of wild-type PTEN degradation. Mol Cancer Res 2014;12:1621-1634. [PMID: 25009292 DOI: 10.1158/1541-7786.mcr-14-0018] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
26
Dhifli W, Saidi R, Nguifo EM. Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities. J Comput Biol 2014;21:162-72. [DOI: 10.1089/cmb.2013.0092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
27
Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW. KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res 2013;42:D389-95. [PMID: 24271397 PMCID: PMC3964971 DOI: 10.1093/nar/gkt1199] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
28
Holder A, Simon J, Strauser J, Taylor J, Shibberu Y. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust. BIOLOGY 2013;2:1296-310. [PMID: 24833226 PMCID: PMC4009789 DOI: 10.3390/biology2041296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/23/2013] [Accepted: 11/08/2013] [Indexed: 11/16/2022]
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