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Number Cited by Other Article(s)
51
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity. Sci Rep 2020;10:1278. [PMID: 31992738 PMCID: PMC6987227 DOI: 10.1038/s41598-020-57778-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022]  Open
52
Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization. Nat Commun 2020;11:297. [PMID: 31941882 PMCID: PMC6962383 DOI: 10.1038/s41467-019-13895-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/28/2019] [Indexed: 11/09/2022]  Open
53
Kamal H, Minhas FUAA, Tripathi D, Abbasi WA, Hamza M, Mustafa R, Khan MZ, Mansoor S, Pappu HR, Amin I. βC1, pathogenicity determinant encoded by Cotton leaf curl Multan betasatellite, interacts with calmodulin-like protein 11 (Gh-CML11) in Gossypium hirsutum. PLoS One 2019;14:e0225876. [PMID: 31794580 PMCID: PMC6890265 DOI: 10.1371/journal.pone.0225876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 11/14/2019] [Indexed: 01/14/2023]  Open
54
Raghav PK, Kumar R, Kumar V, Raghava GPS. Docking-based approach for identification of mutations that disrupt binding between Bcl-2 and Bax proteins: Inducing apoptosis in cancer cells. Mol Genet Genomic Med 2019;7:e910. [PMID: 31490001 PMCID: PMC6825947 DOI: 10.1002/mgg3.910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/09/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022]  Open
55
Zhai Y, Yu X, Zhu Z, Wang P, Meng Y, Zhao Q, Li J, Chen J. Nuclear-Cytoplasmic Coevolution Analysis of RuBisCO in Synthesized Cucumis Allopolyploid. Genes (Basel) 2019;10:genes10110869. [PMID: 31671713 PMCID: PMC6895982 DOI: 10.3390/genes10110869] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 01/03/2023]  Open
56
Santos Pereira-Dutra F, Cancela M, Valandro Meneghetti B, Bunselmeyer Ferreira H, Mariante Monteiro K, Zaha A. Functional characterization of the translation initiation factor eIF4E of Echinococcus granulosus. Parasitol Res 2019;118:2843-2855. [PMID: 31401657 DOI: 10.1007/s00436-019-06421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/02/2019] [Indexed: 01/24/2023]
57
Chen M, Ju CJT, Zhou G, Chen X, Zhang T, Chang KW, Zaniolo C, Wang W. Multifaceted protein-protein interaction prediction based on Siamese residual RCNN. Bioinformatics 2019;35:i305-i314. [PMID: 31510705 PMCID: PMC6681469 DOI: 10.1093/bioinformatics/btz328] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
58
Kamal H, Minhas FUAA, Farooq M, Tripathi D, Hamza M, Mustafa R, Khan MZ, Mansoor S, Pappu HR, Amin I. In silico Prediction and Validations of Domains Involved in Gossypium hirsutum SnRK1 Protein Interaction With Cotton Leaf Curl Multan Betasatellite Encoded βC1. FRONTIERS IN PLANT SCIENCE 2019;10:656. [PMID: 31191577 PMCID: PMC6546731 DOI: 10.3389/fpls.2019.00656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/01/2019] [Indexed: 05/19/2023]
59
Lee ACL, Harris JL, Khanna KK, Hong JH. A Comprehensive Review on Current Advances in Peptide Drug Development and Design. Int J Mol Sci 2019;20:ijms20102383. [PMID: 31091705 PMCID: PMC6566176 DOI: 10.3390/ijms20102383] [Citation(s) in RCA: 417] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022]  Open
60
Galgóczy L, Yap A, Marx F. Cysteine-Rich Antifungal Proteins from Filamentous Fungi are Promising Bioactive Natural Compounds in Anti-Candida Therapy. Isr J Chem 2019;59:360-370. [PMID: 31680702 PMCID: PMC6813639 DOI: 10.1002/ijch.201800168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022]
61
Dutta S, Sinha A, Dasgupta S, Mukherjee AK. Binding of a Naja naja venom acidic phospholipase A2 cognate complex to membrane-bound vimentin of rat L6 cells: Implications in cobra venom-induced cytotoxicity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019;1861:958-977. [PMID: 30776333 DOI: 10.1016/j.bbamem.2019.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 01/28/2023]
62
Kovács R, Holzknecht J, Hargitai Z, Papp C, Farkas A, Borics A, Tóth L, Váradi G, Tóth GK, Kovács I, Dubrac S, Majoros L, Marx F, Galgóczy L. In Vivo Applicability of Neosartorya fischeri Antifungal Protein 2 (NFAP2) in Treatment of Vulvovaginal Candidiasis. Antimicrob Agents Chemother 2019;63:e01777-18. [PMID: 30478163 PMCID: PMC6355578 DOI: 10.1128/aac.01777-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/12/2018] [Indexed: 12/13/2022]  Open
63
Abbasi WA, Asif A, Ben-Hur A, Minhas FUAA. Learning protein binding affinity using privileged information. BMC Bioinformatics 2018;19:425. [PMID: 30442086 PMCID: PMC6238365 DOI: 10.1186/s12859-018-2448-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/25/2018] [Indexed: 01/04/2023]  Open
64
TROP-2 exhibits tumor suppressive functions in cervical cancer by dual inhibition of IGF-1R and ALK signaling. Gynecol Oncol 2018;152:185-193. [PMID: 30429055 DOI: 10.1016/j.ygyno.2018.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/28/2022]
65
Lu B, Li C, Chen Q, Song J. ProBAPred: Inferring protein–protein binding affinity by incorporating protein sequence and structural features. J Bioinform Comput Biol 2018;16:1850011. [PMID: 29954286 DOI: 10.1142/s0219720018500117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
66
Jiang L, Liu G, Liu H, Han J, Liu Z, Ma H. Molecular weight impact on the mechanical forces between hyaluronan and its receptor. Carbohydr Polym 2018;197:326-336. [PMID: 30007620 DOI: 10.1016/j.carbpol.2018.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
67
Hadi-Alijanvand H, Rouhani M. Partner-Specific Prediction of Protein-Dimer Stability from Unbound Structure of Monomer. J Chem Inf Model 2018;58:733-745. [PMID: 29444397 DOI: 10.1021/acs.jcim.7b00606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
68
Jemimah S, Gromiha MM. Exploring additivity effects of double mutations on the binding affinity of protein-protein complexes. Proteins 2018;86:536-547. [DOI: 10.1002/prot.25472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/10/2018] [Accepted: 01/26/2018] [Indexed: 11/06/2022]
69
Smith JK, Jiang S, Pfaendtner J. Redefining the Protein-Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein-Protein Binding Affinity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017;33:11511-11517. [PMID: 28850233 DOI: 10.1021/acs.langmuir.7b02438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
70
Phelix CF, Bourdon AK, Villareal G, LeBaron RG. Modeling non-clinical and clinical drug tests in Gaucher disease. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017;2016:1434-1438. [PMID: 28268595 DOI: 10.1109/embc.2016.7590978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
71
Rangel CK, Parizi LF, Sabadin GA, Costa EP, Romeiro NC, Isezaki M, Githaka NW, Seixas A, Logullo C, Konnai S, Ohashi K, da Silva Vaz I. Molecular and structural characterization of novel cystatins from the taiga tick Ixodes persulcatus. Ticks Tick Borne Dis 2017;8:432-441. [PMID: 28174118 DOI: 10.1016/j.ttbdis.2017.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/27/2017] [Accepted: 01/27/2017] [Indexed: 11/19/2022]
72
Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;128:33-38. [PMID: 28069340 DOI: 10.1016/j.pbiomolbio.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/09/2023]
73
Important amino acid residues involved in folding and binding of protein–protein complexes. Int J Biol Macromol 2017;94:438-444. [DOI: 10.1016/j.ijbiomac.2016.10.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/15/2016] [Indexed: 01/12/2023]
74
Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes. Methods Mol Biol 2017;1484:237-253. [PMID: 27787830 DOI: 10.1007/978-1-4939-6406-2_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
75
Swanson J, Audie J. An unexpected way forward: towards a more accurate and rigorous protein-protein binding affinity scoring function by eliminating terms from an already simple scoring function. J Biomol Struct Dyn 2016;36:83-97. [PMID: 27989231 DOI: 10.1080/07391102.2016.1268974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
76
Gromiha MM, Yugandhar K, Jemimah S. Protein-protein interactions: scoring schemes and binding affinity. Curr Opin Struct Biol 2016;44:31-38. [PMID: 27866112 DOI: 10.1016/j.sbi.2016.10.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/30/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023]
77
Nagarajan R, Archana A, Thangakani AM, Jemimah S, Velmurugan D, Gromiha MM. PDBparam: Online Resource for Computing Structural Parameters of Proteins. Bioinform Biol Insights 2016;10:73-80. [PMID: 27330281 PMCID: PMC4909059 DOI: 10.4137/bbi.s38423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/20/2016] [Accepted: 04/24/2016] [Indexed: 02/07/2023]  Open
78
Rigid-Docking Approaches to Explore Protein-Protein Interaction Space. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016;160:33-55. [PMID: 27830312 DOI: 10.1007/10_2016_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
79
Srinivasulu YS, Wang JR, Hsu KT, Tsai MJ, Charoenkwan P, Huang WL, Huang HL, Ho SY. Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes. BMC Bioinformatics 2015;16 Suppl 18:S14. [PMID: 26681483 PMCID: PMC4682391 DOI: 10.1186/1471-2105-16-s18-s14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
80
Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures. J Membr Biol 2015;249:141-53. [DOI: 10.1007/s00232-015-9856-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
81
Sowmya G, Breen EJ, Ranganathan S. Linking structural features of protein complexes and biological function. Protein Sci 2015;24:1486-94. [PMID: 26131659 DOI: 10.1002/pro.2736] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 11/11/2022]
82
Petukh M, Li M, Alexov E. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLoS Comput Biol 2015;11:e1004276. [PMID: 26146996 PMCID: PMC4492929 DOI: 10.1371/journal.pcbi.1004276] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022]  Open
83
Yugandhar K, Gromiha MM. Response to the comment on 'protein-protein binding affinity prediction from amino acid sequence'. Bioinformatics 2014;31:978. [PMID: 25505089 DOI: 10.1093/bioinformatics/btu821] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
84
Moal IH, Fernández-Recio J. Comment on 'protein-protein binding affinity prediction from amino acid sequence'. Bioinformatics 2014;31:614-5. [PMID: 25381451 DOI: 10.1093/bioinformatics/btu682] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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