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For: Hopf TA, Green AG, Schubert B, Mersmann S, Schärfe CPI, Ingraham JB, Toth-Petroczy A, Brock K, Riesselman AJ, Palmedo P, Kang C, Sheridan R, Draizen EJ, Dallago C, Sander C, Marks DS. The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics 2020;35:1582-1584. [PMID: 30304492 PMCID: PMC6499242 DOI: 10.1093/bioinformatics/bty862] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/06/2018] [Accepted: 10/08/2018] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Liu J, Neupane P, Cheng J. Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16. Proteins 2025. [PMID: 40452318 DOI: 10.1002/prot.26850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 05/06/2025] [Accepted: 05/23/2025] [Indexed: 06/11/2025]
2
Ma X, Zhu K, Wang K, Liao W, Yang X, Yu W, Wang W, Han F. Improvement of Catalytic Activity and Thermostability of Alginate Lyase VxAly7B-CM via Rational Computational Design Strategies. Mar Drugs 2025;23:198. [PMID: 40422788 DOI: 10.3390/md23050198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/26/2025] [Accepted: 04/26/2025] [Indexed: 05/28/2025]  Open
3
Kumar SP, Nadendla EK, Malireddi RKS, Haque SA, Mall R, Neuwald AF, Kanneganti TD. Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis. Mol Biol Evol 2025;42:msaf096. [PMID: 40277230 PMCID: PMC12066828 DOI: 10.1093/molbev/msaf096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 04/09/2025] [Accepted: 04/15/2025] [Indexed: 04/26/2025]  Open
4
Sanyal D, Shivram A, Pandey D, Banerjee S, Uversky VN, Muzata D, Chivukula AS, Jasuja R, Chattopadhyay K, Chowdhury S. Mapping dihydropteroate synthase evolvability through identification of a novel evolutionarily critical substructure. Int J Biol Macromol 2025;311:143325. [PMID: 40254194 DOI: 10.1016/j.ijbiomac.2025.143325] [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: 12/29/2024] [Revised: 03/28/2025] [Accepted: 04/17/2025] [Indexed: 04/22/2025]
5
Miller ST, Macdonald CB, Raman S. Understanding, inhibiting, and engineering membrane transporters with high-throughput mutational screens. Cell Chem Biol 2025;32:529-541. [PMID: 40168989 DOI: 10.1016/j.chembiol.2025.03.003] [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: 09/07/2024] [Revised: 01/20/2025] [Accepted: 03/10/2025] [Indexed: 04/03/2025]
6
Baeza J, Bedoya M, Cruz P, Ojeda P, Adasme-Carreño F, Cerda O, González W. Main methods and tools for peptide development based on protein-protein interactions (PPIs). Biochem Biophys Res Commun 2025;758:151623. [PMID: 40121967 DOI: 10.1016/j.bbrc.2025.151623] [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: 09/29/2024] [Revised: 03/05/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025]
7
Liu J, Neupane P, Cheng J. Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.06.641913. [PMID: 40161604 PMCID: PMC11952293 DOI: 10.1101/2025.03.06.641913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
8
Luppino F, Lenz S, Chow CFW, Toth-Petroczy A. Deep learning tools predict variants in disordered regions with lower sensitivity. BMC Genomics 2025;26:367. [PMID: 40221640 PMCID: PMC11992697 DOI: 10.1186/s12864-025-11534-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 03/27/2025] [Indexed: 04/14/2025]  Open
9
Meng Y, Zhang Z, Zhou C, Tang X, Hu X, Tian G, Yang J, Yao Y. Protein structure prediction via deep learning: an in-depth review. Front Pharmacol 2025;16:1498662. [PMID: 40248099 PMCID: PMC12003282 DOI: 10.3389/fphar.2025.1498662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 02/28/2025] [Indexed: 04/19/2025]  Open
10
Mychack A, Evans D, Gilles T, James MJ, Walker S. Staphylococcus aureus uses a GGDEF protein to recruit diacylglycerol kinase to the membrane for lipid recycling. Proc Natl Acad Sci U S A 2025;122:e2414696122. [PMID: 40100631 PMCID: PMC11962490 DOI: 10.1073/pnas.2414696122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 02/03/2025] [Indexed: 03/20/2025]  Open
11
Xing E, Zhang J, Wang S, Cheng X. Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2. RESEARCH SQUARE 2025:rs.3.rs-6087969. [PMID: 40092441 PMCID: PMC11908349 DOI: 10.21203/rs.3.rs-6087969/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
12
Han B, Zhang Y, Li L, Gong X, Xia K. TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment. Brief Bioinform 2025;26:bbaf083. [PMID: 40062613 PMCID: PMC11891663 DOI: 10.1093/bib/bbaf083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/11/2025] [Accepted: 02/17/2025] [Indexed: 05/13/2025]  Open
13
Song J, Qiao J, Cheng Z, Guo J, Wang Q, Zhou Z, Han L. Computational design of coevolutionary residues for improved stability and activity of nitrile hydratase. Biochem Biophys Res Commun 2025;750:151400. [PMID: 39889624 DOI: 10.1016/j.bbrc.2025.151400] [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: 01/18/2025] [Accepted: 01/25/2025] [Indexed: 02/03/2025]
14
Sun J, Ru J, Cribbs AP, Xiong D. PyPropel: a Python-based tool for efficiently processing and characterising protein data. BMC Bioinformatics 2025;26:70. [PMID: 40025421 PMCID: PMC11871610 DOI: 10.1186/s12859-025-06079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Accepted: 02/10/2025] [Indexed: 03/04/2025]  Open
15
Nelson MG, Talavera D. Identification of coevolving positions by ancestral reconstruction. Commun Biol 2025;8:329. [PMID: 40021815 PMCID: PMC11871020 DOI: 10.1038/s42003-025-07676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 02/05/2025] [Indexed: 03/03/2025]  Open
16
Forrest B, Derbel H, Zhao Z, Liu Q. MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants. Comput Struct Biotechnol J 2025;27:672-681. [PMID: 40070521 PMCID: PMC11894328 DOI: 10.1016/j.csbj.2025.02.012] [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: 11/25/2024] [Revised: 02/10/2025] [Accepted: 02/17/2025] [Indexed: 03/14/2025]  Open
17
Thornton BW, Weissman RF, Tran RV, Duong BT, Rodriguez JE, Terrace CI, Groover ED, Park JU, Tartaglia J, Doudna JA, Savage DF. Latent activity in TnpB revealed by mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.11.637750. [PMID: 39990302 PMCID: PMC11844463 DOI: 10.1101/2025.02.11.637750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
18
Gelman S, Johnson B, Freschlin C, Sharma A, D'Costa S, Peters J, Gitter A, Romero PA. Biophysics-based protein language models for protein engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.03.15.585128. [PMID: 38559182 PMCID: PMC10980077 DOI: 10.1101/2024.03.15.585128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
19
Hermans P, Tsishyn M, Schwersensky M, Rooman M, Pucci F. Exploring Evolution to Uncover Insights Into Protein Mutational Stability. Mol Biol Evol 2025;42:msae267. [PMID: 39786559 PMCID: PMC11721782 DOI: 10.1093/molbev/msae267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 11/27/2024] [Accepted: 11/28/2024] [Indexed: 01/12/2025]  Open
20
Chu HY, Peng J, Mou Y, Wong ASL. Quantifying Protein-Nucleic Acid Interactions for Engineering Useful CRISPR-Cas9 Genome-Editing Variants. Methods Mol Biol 2025;2870:227-243. [PMID: 39543038 DOI: 10.1007/978-1-0716-4213-9_12] [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] [Indexed: 11/17/2024]
21
Mikołajczyk K, Wróblewski K, Kmiecik S. Delving into human α1,4-galactosyltransferase acceptor specificity: The role of enzyme dimerization. Biochem Biophys Res Commun 2024;736:150486. [PMID: 39111055 DOI: 10.1016/j.bbrc.2024.150486] [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: 06/03/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 11/10/2024]
22
Yehorova D, Di Geronimo B, Robinson M, Kasson PM, Kamerlin SCL. Using residue interaction networks to understand protein function and evolution and to engineer new proteins. Curr Opin Struct Biol 2024;89:102922. [PMID: 39332048 DOI: 10.1016/j.sbi.2024.102922] [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: 06/22/2024] [Revised: 08/21/2024] [Accepted: 09/02/2024] [Indexed: 09/29/2024]
23
Zhang C, Wang Q, Li Y, Teng A, Hu G, Wuyun Q, Zheng W. The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction. Biomolecules 2024;14:1531. [PMID: 39766238 PMCID: PMC11673352 DOI: 10.3390/biom14121531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/24/2024] [Accepted: 11/27/2024] [Indexed: 01/11/2025]  Open
24
Gao W, Jing Z, Meng Y, Liu Q, Wang H, Wei D. Inside-Out Rational Design of Ornithine Cyclodeaminase RlOCD from Rhizobium leguminosarum by a Multiregion Synergy Strategy for Efficient Synthesis of l-Pipecolic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:25782-25790. [PMID: 39387484 DOI: 10.1021/acs.jafc.4c06331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
25
Sverak HE, Yaeger LN, Worrall LJ, Vacariu CM, Glenwright AJ, Vuckovic M, Al Azawi ZD, Lamers RP, Marko VA, Skorupski C, Soni AS, Tanner ME, Burrows LL, Strynadka NC. Cryo-EM characterization of the anydromuropeptide permease AmpG central to bacterial fitness and β-lactam antibiotic resistance. Nat Commun 2024;15:9936. [PMID: 39548104 PMCID: PMC11568325 DOI: 10.1038/s41467-024-54219-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 11/03/2024] [Indexed: 11/17/2024]  Open
26
Souza Amado de Carvalho R, Rasel MSI, Khandelwal NK, Tomasiak TM. Cryo-EM reveals a phosphorylated R-domain envelops the NBD1 catalytic domain in an ABC transporter. Life Sci Alliance 2024;7:e202402779. [PMID: 39209537 PMCID: PMC11361370 DOI: 10.26508/lsa.202402779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]  Open
27
Karagöl A, Karagöl T, Li M, Zhang S. Inhibitory Potential of the Truncated Isoforms on Glutamate Transporter Oligomerization Identified by Computational Analysis of Gene-Centric Isoform Maps. Pharm Res 2024;41:2173-2187. [PMID: 39487385 PMCID: PMC11599315 DOI: 10.1007/s11095-024-03786-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 10/14/2024] [Indexed: 11/04/2024]
28
Li Y, Wang Y, Tan YQ, Yue Q, Guo Y, Yan R, Meng L, Zhai H, Tong L, Yuan Z, Li W, Wang C, Han S, Ren S, Yan Y, Wang W, Gao L, Tan C, Hu T, Zhang H, Liu L, Yang P, Jiang W, Ye Y, Tan H, Wang Y, Lu C, Li X, Xie J, Yuan G, Cui Y, Shen B, Wang C, Guan Y, Li W, Shi Q, Lin G, Ni T, Sun Z, Ye L, Vourekas A, Guo X, Lin M, Zheng K. The landscape of RNA binding proteins in mammalian spermatogenesis. Science 2024;386:eadj8172. [PMID: 39208083 DOI: 10.1126/science.adj8172] [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: 07/19/2023] [Revised: 04/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
29
Draizen EJ, Veretnik S, Mura C, Bourne PE. Deep generative models of protein structure uncover distant relationships across a continuous fold space. Nat Commun 2024;15:8094. [PMID: 39294145 PMCID: PMC11410806 DOI: 10.1038/s41467-024-52020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/23/2024] [Indexed: 09/20/2024]  Open
30
Zhang T, Tian S, Gao Z, Li Y, Jia H. Engineering an Ancestral Glycosyltransferase for Biosynthesis of 2-Phenylethyl-β-d-Glucopyranoside and Salidroside. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:19966-19976. [PMID: 39189841 DOI: 10.1021/acs.jafc.4c04381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
31
Luo J, Song C, Cui W, Wang Q, Zhou Z, Han L. Precise redesign for improving enzyme robustness based on coevolutionary analysis and multidimensional virtual screening. Chem Sci 2024:d4sc02058h. [PMID: 39257856 PMCID: PMC11382147 DOI: 10.1039/d4sc02058h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/27/2024] [Indexed: 09/12/2024]  Open
32
Tang X, Ortner NJ, Nikonishyna YV, Fernández-Quintero ML, Kokot J, Striessnig J, Liedl KR. Pathogenicity of de novo CACNA1D Ca2+ channel variants predicted from sequence co-variation. Eur J Hum Genet 2024;32:1065-1073. [PMID: 38553610 PMCID: PMC11369236 DOI: 10.1038/s41431-024-01594-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/02/2024] [Accepted: 03/12/2024] [Indexed: 09/04/2024]  Open
33
Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci 2024;33:e5097. [PMID: 39145402 PMCID: PMC11325166 DOI: 10.1002/pro.5097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 08/16/2024]
34
Almhjell PJ, Johnston KE, Porter NJ, Kennemur JL, Bhethanabotla VC, Ducharme J, Arnold FH. The β-subunit of tryptophan synthase is a latent tyrosine synthase. Nat Chem Biol 2024;20:1086-1093. [PMID: 38744987 PMCID: PMC11288773 DOI: 10.1038/s41589-024-01619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
35
Ding K, Chin M, Zhao Y, Huang W, Mai BK, Wang H, Liu P, Yang Y, Luo Y. Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering. Nat Commun 2024;15:6392. [PMID: 39080249 PMCID: PMC11289365 DOI: 10.1038/s41467-024-50698-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024]  Open
36
Otteson L, Nagy G, Kunkel J, Kodis G, Zheng W, Bignon C, Longhi S, Grubmüller H, Vaiana AC, Vaiana SM. Transient Non-local Interactions Dominate the Dynamics of Measles Virus NTAIL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604679. [PMID: 39091801 PMCID: PMC11291014 DOI: 10.1101/2024.07.22.604679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
37
Basu S, Subedi U, Tonelli M, Afshinpour M, Tiwari N, Fuentes EJ, Chakravarty S. Assessing the functional roles of coevolving PHD finger residues. Protein Sci 2024;33:e5065. [PMID: 38923615 PMCID: PMC11201814 DOI: 10.1002/pro.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024]
38
Martí JM, Hsu C, Rochereau C, Xu C, Blazejewski T, Nisonoff H, Leonard SP, Kang-Yun CS, Chlebek J, Ricci DP, Park D, Wang H, Listgarten J, Jiao Y, Allen JE. GENTANGLE: integrated computational design of gene entanglements. Bioinformatics 2024;40:btae380. [PMID: 38905502 PMCID: PMC11251573 DOI: 10.1093/bioinformatics/btae380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/23/2024]  Open
39
Fram B, Su Y, Truebridge I, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler MA, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nat Commun 2024;15:5141. [PMID: 38902262 PMCID: PMC11190266 DOI: 10.1038/s41467-024-49119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/24/2024] [Indexed: 06/22/2024]  Open
40
Chakraborty J, Poddar S, Dutta S, Bahulekar V, Harne S, Srinivasan R, Gayathri P. Dynamics of interdomain rotation facilitates FtsZ filament assembly. J Biol Chem 2024;300:107336. [PMID: 38718863 PMCID: PMC11157280 DOI: 10.1016/j.jbc.2024.107336] [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: 03/09/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]  Open
41
Nixon C, Lim SA, Sternke M, Barrick D, Harms MJ, Marqusee S. The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins. Protein Sci 2024;33:e5011. [PMID: 38747388 PMCID: PMC11094778 DOI: 10.1002/pro.5011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
42
Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structural basis of ligand specificity and channel activation in an insect gustatory receptor. Cell Rep 2024;43:114035. [PMID: 38573859 PMCID: PMC11100771 DOI: 10.1016/j.celrep.2024.114035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/26/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]  Open
43
Dibley K, Jost M, McIntosh R, Lagudah E, Zhang P. The wheat stripe rust resistance gene YrNAM is Yr10. Nat Commun 2024;15:3291. [PMID: 38632235 PMCID: PMC11024124 DOI: 10.1038/s41467-024-47513-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024]  Open
44
MacGowan SA, Madeira F, Britto-Borges T, Barton GJ. A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites. Commun Biol 2024;7:447. [PMID: 38605212 PMCID: PMC11009406 DOI: 10.1038/s42003-024-06117-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]  Open
45
Bibik P, Alibai S, Pandini A, Dantu SC. PyCoM: a python library for large-scale analysis of residue-residue coevolution data. Bioinformatics 2024;40:btae166. [PMID: 38532297 PMCID: PMC11009027 DOI: 10.1093/bioinformatics/btae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 03/28/2024]  Open
46
de Carvalho RSA, Rasel SI, Khandelwal NK, Tomasiak TM. Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583773. [PMID: 38496555 PMCID: PMC10942426 DOI: 10.1101/2024.03.06.583773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
47
Perreault M, Means J, Gerson E, James M, Cotton S, Bergeron CG, Simon M, Carlin DA, Schmidt N, Moore TC, Blasbalg J, Sondheimer N, Ndugga-Kabuye K, Denney WS, Isabella VM, Lubkowicz D, Brennan A, Hava DL. The live biotherapeutic SYNB1353 decreases plasma methionine via directed degradation in animal models and healthy volunteers. Cell Host Microbe 2024;32:382-395.e10. [PMID: 38309259 DOI: 10.1016/j.chom.2024.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/05/2024]
48
Landerer C, Poehls J, Toth-Petroczy A. Fitness Effects of Phenotypic Mutations at Proteome-Scale Reveal Optimality of Translation Machinery. Mol Biol Evol 2024;41:msae048. [PMID: 38421032 PMCID: PMC10939442 DOI: 10.1093/molbev/msae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]  Open
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Yehorova D, Crean RM, Kasson PM, Kamerlin SCL. Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families. Protein Sci 2024;33:e4911. [PMID: 38358258 PMCID: PMC10868456 DOI: 10.1002/pro.4911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
50
Ektefaie Y, Shen A, Bykova D, Marin M, Zitnik M, Farhat M. Evaluating generalizability of artificial intelligence models for molecular datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581982. [PMID: 38464295 PMCID: PMC10925170 DOI: 10.1101/2024.02.25.581982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
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