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For: Li Y, Middaugh CR, Fang J. A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. BMC Bioinformatics 2010;11:62. [PMID: 20109199 PMCID: PMC3098108 DOI: 10.1186/1471-2105-11-62] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 01/28/2010] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Miao H, Xiang X, Han N, Wu Q, Huang Z. Improving the Thermostability of Serine Protease PB92 from Bacillus alcalophilus via Site-Directed Mutagenesis Based on Semi-Rational Design. Foods 2023;12:3081. [PMID: 37628080 PMCID: PMC10453622 DOI: 10.3390/foods12163081] [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: 07/20/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]  Open
2
Fang J. Predicting thermostability difference between cellular protein orthologs. Bioinformatics 2023;39:btad504. [PMID: 37572303 PMCID: PMC10457660 DOI: 10.1093/bioinformatics/btad504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/02/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023]  Open
3
Hait S, Basu S, Kundu S. Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy. J Biomol Struct Dyn 2023;41:1745-1752. [PMID: 34996344 DOI: 10.1080/07391102.2021.2024258] [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: 02/02/2023]
4
Kumar S, Duggineni VK, Singhania V, Misra SP, Deshpande PA. Unravelling and Quantifying the Biophysical– Biochemical Descriptors Governing Protein Thermostability by Machine Learning. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
5
Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity. Nat Commun 2022;13:7850. [PMID: 36543766 PMCID: PMC9772341 DOI: 10.1038/s41467-022-35237-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]  Open
6
Wang D, Li J, Sun Y, Ding X, Zhang X, Liu S, Han B, Wang H, Duan X, Sun T. A Machine Learning Model for Accurate Prediction of Sepsis in ICU Patients. Front Public Health 2021;9:754348. [PMID: 34722452 PMCID: PMC8553999 DOI: 10.3389/fpubh.2021.754348] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022]  Open
7
Kozuka K, Nakano S, Asano Y, Ito S. Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations. Biochemistry 2021;60:2309-2319. [PMID: 34254784 DOI: 10.1021/acs.biochem.1c00309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
8
Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021;371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
9
Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol 2020;643:149-179. [PMID: 32896279 DOI: 10.1016/bs.mie.2020.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
10
Gado JE, Beckham GT, Payne CM. Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning. J Chem Inf Model 2020;60:4098-4107. [DOI: 10.1021/acs.jcim.0c00489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
11
Sauer DB, Wang DN. Predicting the optimal growth temperatures of prokaryotes using only genome derived features. Bioinformatics 2020;35:3224-3231. [PMID: 30689741 DOI: 10.1093/bioinformatics/btz059] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/20/2018] [Accepted: 01/22/2019] [Indexed: 11/14/2022]  Open
12
Hait S, Mallik S, Basu S, Kundu S. Finding the generalized molecular principles of protein thermal stability. Proteins 2019;88:788-808. [PMID: 31872464 DOI: 10.1002/prot.25866] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/14/2019] [Indexed: 11/09/2022]
13
Consensus sequence design as a general strategy to create hyperstable, biologically active proteins. Proc Natl Acad Sci U S A 2019;116:11275-11284. [PMID: 31110018 DOI: 10.1073/pnas.1816707116] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
14
Tian B, Talukder SK, Fu J, Fritz AK, Trick HN. Expression of a rice soluble starch synthase gene in transgenic wheat improves the grain yield under heat stress conditions. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2018;54:216-227. [PMID: 29780215 PMCID: PMC5954006 DOI: 10.1007/s11627-018-9893-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/16/2018] [Indexed: 05/04/2023]
15
Tang H, Cui F, Liu L, Li Y. Predictive models for tyrosinase inhibitors: Challenges from heterogeneous activity data determined by different experimental protocols. Comput Biol Chem 2018;73:79-84. [PMID: 29471263 DOI: 10.1016/j.compbiolchem.2018.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/02/2018] [Accepted: 02/08/2018] [Indexed: 10/18/2022]
16
Sawle L, Huihui J, Ghosh K. All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation. J Chem Theory Comput 2017;13:5065-5075. [DOI: 10.1021/acs.jctc.7b00545] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Leng F, Xu C, Xia XY, Pan XM. Establishing knowledge on the sequence arrangement pattern of nucleated protein folding. PLoS One 2017;12:e0173583. [PMID: 28273143 PMCID: PMC5342263 DOI: 10.1371/journal.pone.0173583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/22/2017] [Indexed: 11/21/2022]  Open
18
Sawle L, Ghosh K. A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins. J Chem Phys 2016;143:085101. [PMID: 26328871 DOI: 10.1063/1.4929391] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
19
Wahome N, Sully E, Singer C, Thomas JC, Hu L, Joshi SB, Volkin DB, Fang J, Karanicolas J, Jacobs DJ, Mantis NJ, Middaugh CR. Novel Ricin Subunit Antigens With Enhanced Capacity to Elicit Toxin-Neutralizing Antibody Responses in Mice. J Pharm Sci 2016;105:1603-1613. [PMID: 26987947 PMCID: PMC4846473 DOI: 10.1016/j.xphs.2016.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/26/2016] [Accepted: 02/09/2016] [Indexed: 02/07/2023]
20
Insights into the molecular basis of piezophilic adaptation: Extraction of piezophilic signatures. J Theor Biol 2015;390:117-26. [PMID: 26656108 DOI: 10.1016/j.jtbi.2015.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 11/06/2015] [Accepted: 11/21/2015] [Indexed: 11/20/2022]
21
Nath A, Subbiah K. Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier. Comput Biol Chem 2014;53PB:198-203. [PMID: 25462328 DOI: 10.1016/j.compbiolchem.2014.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/02/2014] [Accepted: 10/06/2014] [Indexed: 11/19/2022]
22
Talukder SK, Babar MA, Vijayalakshmi K, Poland J, Prasad PVV, Bowden R, Fritz A. Mapping QTL for the traits associated with heat tolerance in wheat (Triticum aestivum L.). BMC Genet 2014. [PMID: 25384418 DOI: 10.1186/s12863-014-0097-94] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]  Open
23
Talukder SK, Babar MA, Vijayalakshmi K, Poland J, Prasad PVV, Bowden R, Fritz A. Mapping QTL for the traits associated with heat tolerance in wheat (Triticum aestivum L.). BMC Genet 2014. [PMID: 25384418 DOI: 10.1186/s12863-014-00974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]  Open
24
Talukder SK, Babar MA, Vijayalakshmi K, Poland J, Prasad PVV, Bowden R, Fritz A. Mapping QTL for the traits associated with heat tolerance in wheat (Triticum aestivum L.). BMC Genet 2014;15:97. [PMID: 25384418 PMCID: PMC4234900 DOI: 10.1186/s12863-014-0097-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022]  Open
25
Prediction of the determinants of thermal stability by linear discriminant analysis: the case of the glutamate dehydrogenase protein family. J Theor Biol 2014;357:160-8. [PMID: 24853273 DOI: 10.1016/j.jtbi.2014.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 11/21/2022]
26
Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A. De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 2013;14:563. [PMID: 23957668 PMCID: PMC3765226 DOI: 10.1186/1471-2164-14-563] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/13/2013] [Indexed: 01/15/2023]  Open
27
Graham LD, Glattauer V, Li D, Tyler MJ, Ramshaw JAM. The adhesive skin exudate of Notaden bennetti frogs (Anura: Limnodynastidae) has similarities to the prey capture glue of Euperipatoides sp. velvet worms (Onychophora: Peripatopsidae). Comp Biochem Physiol B Biochem Mol Biol 2013;165:250-9. [PMID: 23665109 DOI: 10.1016/j.cbpb.2013.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/09/2013] [Accepted: 04/30/2013] [Indexed: 11/30/2022]
28
Thomas JC, O'Hara JM, Hu L, Gao FP, Joshi SB, Volkin DB, Brey RN, Fang J, Karanicolas J, Mantis NJ, Middaugh CR. Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin A chain subunit vaccine antigen. Hum Vaccin Immunother 2013;9:744-52. [PMID: 23563512 DOI: 10.4161/hv.22998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
29
Holder T, Basquin C, Ebert J, Randel N, Jollivet D, Conti E, Jékely G, Bono F. Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability. Biol Direct 2013;8:2. [PMID: 23324115 PMCID: PMC3564776 DOI: 10.1186/1745-6150-8-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/11/2013] [Indexed: 12/27/2022]  Open
30
Li Y, Fang J. PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One 2012;7:e47247. [PMID: 23077576 PMCID: PMC3471942 DOI: 10.1371/journal.pone.0047247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]  Open
31
Fang Y, Middaugh CR, Fang J. In silico classification of proteins from acidic and neutral cytoplasms. PLoS One 2012;7:e45585. [PMID: 23049817 PMCID: PMC3458925 DOI: 10.1371/journal.pone.0045585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 08/23/2012] [Indexed: 01/05/2023]  Open
32
Li Y, Zhang J, Tai D, Middaugh CR, Zhang Y, Fang J. PROTS: a fragment based protein thermo-stability potential. Proteins 2011;80:81-92. [PMID: 21976375 DOI: 10.1002/prot.23163] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/18/2011] [Accepted: 07/31/2011] [Indexed: 12/30/2022]
33
King AC, Woods M, Liu W, Lu Z, Gill D, Krebs MRH. High-throughput measurement, correlation analysis, and machine-learning predictions for pH and thermal stabilities of Pfizer-generated antibodies. Protein Sci 2011;20:1546-57. [PMID: 21710487 PMCID: PMC3190149 DOI: 10.1002/pro.680] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 05/17/2011] [Accepted: 06/12/2011] [Indexed: 12/16/2022]
34
Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem Biophys Res Commun 2010;396:736-41. [PMID: 20451495 DOI: 10.1016/j.bbrc.2010.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 05/02/2010] [Indexed: 11/22/2022]
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