• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4602587)   Today's Articles (2338)   Subscriber (49368)
For: Müller AT, Hiss JA, Schneider G. Recurrent Neural Network Model for Constructive Peptide Design. J Chem Inf Model 2018;58:472-479. [PMID: 29355319 DOI: 10.1021/acs.jcim.7b00414] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Number Cited by Other Article(s)
1
Orsi M, Reymond JL. Can large language models predict antimicrobial peptide activity and toxicity? RSC Med Chem 2024;15:2030-2036. [PMID: 38911166 PMCID: PMC11187562 DOI: 10.1039/d4md00159a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/19/2024] [Indexed: 06/25/2024]  Open
2
Liang Q, Liu Z, Liang Z, Zhu C, Li D, Kong Q, Mou H. Development strategies and application of antimicrobial peptides as future alternatives to in-feed antibiotics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;927:172150. [PMID: 38580107 DOI: 10.1016/j.scitotenv.2024.172150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
3
Fukunaga I, Matsukiyo Y, Kaitoh K, Yamanishi Y. Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization. Mol Inform 2024;43:e202300148. [PMID: 38182544 DOI: 10.1002/minf.202300148] [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: 06/20/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 01/07/2024]
4
Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024;30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
5
Tsai CT, Lin CW, Ye GL, Wu SC, Yao P, Lin CT, Wan L, Tsai HHG. Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models. ACS OMEGA 2024;9:9357-9374. [PMID: 38434814 PMCID: PMC10905719 DOI: 10.1021/acsomega.3c08676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
6
Yu H, Wang R, Qiao J, Wei L. Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. J Chem Inf Model 2024;64:316-326. [PMID: 38135439 DOI: 10.1021/acs.jcim.3c01881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
7
Aguilera-Puga MDC, Cancelarich NL, Marani MM, de la Fuente-Nunez C, Plisson F. Accelerating the Discovery and Design of Antimicrobial Peptides with Artificial Intelligence. Methods Mol Biol 2024;2714:329-352. [PMID: 37676607 DOI: 10.1007/978-1-0716-3441-7_18] [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] [Indexed: 09/08/2023]
8
Chang DH, Lee MR, Wang N, Lynn DM, Palecek SP. Establishing Quantifiable Guidelines for Antimicrobial α/β-Peptide Design: A Partial Least-Squares Approach to Improve Antimicrobial Activity and Reduce Mammalian Cell Toxicity. ACS Infect Dis 2023;9:2632-2651. [PMID: 38014670 PMCID: PMC10807133 DOI: 10.1021/acsinfecdis.3c00468] [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] [Indexed: 11/29/2023]
9
Capponi S, Daniels KG. Harnessing the power of artificial intelligence to advance cell therapy. Immunol Rev 2023;320:147-165. [PMID: 37415280 DOI: 10.1111/imr.13236] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
10
Pedron CN, Torres MDT, Oliveira CS, Silva AF, Andrade GP, Wang Y, Pinhal MAS, Cerchiaro G, da Silva Junior PI, da Silva FD, Radhakrishnan R, de la Fuente-Nunez C, Oliveira Junior VX. Molecular hybridization strategy for tuning bioactive peptide function. Commun Biol 2023;6:1067. [PMID: 37857855 PMCID: PMC10587126 DOI: 10.1038/s42003-023-05254-7] [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: 05/18/2022] [Accepted: 08/17/2023] [Indexed: 10/21/2023]  Open
11
Michailidou F. The Scent of Change: Sustainable Fragrances Through Industrial Biotechnology. Chembiochem 2023;24:e202300309. [PMID: 37668275 DOI: 10.1002/cbic.202300309] [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: 04/19/2023] [Revised: 05/29/2023] [Indexed: 09/06/2023]
12
Ahmad B, Achek A, Farooq M, Choi S. Accelerated NLRP3 inflammasome-inhibitory peptide design using a recurrent neural network model and molecular dynamics simulations. Comput Struct Biotechnol J 2023;21:4825-4835. [PMID: 37854633 PMCID: PMC10579963 DOI: 10.1016/j.csbj.2023.09.038] [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: 02/24/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]  Open
13
Arras P, Yoo HB, Pekar L, Clarke T, Friedrich L, Schröter C, Schanz J, Tonillo J, Siegmund V, Doerner A, Krah S, Guarnera E, Zielonka S, Evers A. AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study. Front Mol Biosci 2023;10:1249247. [PMID: 37842638 PMCID: PMC10575757 DOI: 10.3389/fmolb.2023.1249247] [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: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 10/17/2023]  Open
14
Mardikoraem M, Wang Z, Pascual N, Woldring D. Generative models for protein sequence modeling: recent advances and future directions. Brief Bioinform 2023;24:bbad358. [PMID: 37864295 PMCID: PMC10589401 DOI: 10.1093/bib/bbad358] [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: 06/13/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/22/2023]  Open
15
Cesaro A, Bagheri M, Torres MDT, Wan F, de la Fuente-Nunez C. Deep learning tools to accelerate antibiotic discovery. Expert Opin Drug Discov 2023;18:1245-1257. [PMID: 37794737 PMCID: PMC10790350 DOI: 10.1080/17460441.2023.2250721] [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: 05/19/2023] [Accepted: 08/18/2023] [Indexed: 10/06/2023]
16
Lin TT, Yang LY, Lin CY, Wang CT, Lai CW, Ko CF, Shih YH, Chen SH. Intelligent De Novo Design of Novel Antimicrobial Peptides against Antibiotic-Resistant Bacteria Strains. Int J Mol Sci 2023;24:ijms24076788. [PMID: 37047760 PMCID: PMC10095442 DOI: 10.3390/ijms24076788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/24/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]  Open
17
Koutroumpa NM, Papavasileiou KD, Papadiamantis AG, Melagraki G, Afantitis A. A Systematic Review of Deep Learning Methodologies Used in the Drug Discovery Process with Emphasis on In Vivo Validation. Int J Mol Sci 2023;24:6573. [PMID: 37047543 PMCID: PMC10095548 DOI: 10.3390/ijms24076573] [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: 12/18/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]  Open
18
Zouhir A, Souiai O, Harigua E, Cherif A, Chaalia AB, Sebei K. ANTIPSEUDOBASE: Database of Antimicrobial Peptides and Essential Oils Against Pseudomonas. Int J Pept Res Ther 2023. [DOI: 10.1007/s10989-023-10511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
19
Szymczak P, Możejko M, Grzegorzek T, Jurczak R, Bauer M, Neubauer D, Sikora K, Michalski M, Sroka J, Setny P, Kamysz W, Szczurek E. Discovering highly potent antimicrobial peptides with deep generative model HydrAMP. Nat Commun 2023;14:1453. [PMID: 36922490 PMCID: PMC10017685 DOI: 10.1038/s41467-023-36994-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023]  Open
20
Wang X, Yang X, Wang Q, Meng D. Unnatural amino acids: promising implications for the development of new antimicrobial peptides. Crit Rev Microbiol 2023;49:231-255. [PMID: 35254957 DOI: 10.1080/1040841x.2022.2047008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
21
Wang Y. Intelligent auxiliary system for music performance under edge computing and long short-term recurrent neural networks. PLoS One 2023;18:e0285496. [PMID: 37155635 PMCID: PMC10166492 DOI: 10.1371/journal.pone.0285496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023]  Open
22
Specific Focus on Antifungal Peptides against Azole Resistant Aspergillus fumigatus: Current Status, Challenges, and Future Perspectives. J Fungi (Basel) 2022;9:jof9010042. [PMID: 36675863 PMCID: PMC9864941 DOI: 10.3390/jof9010042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]  Open
23
Application of a deep generative model produces novel and diverse functional peptides against microbial resistance. Comput Struct Biotechnol J 2022;21:463-471. [PMID: 36618982 PMCID: PMC9804011 DOI: 10.1016/j.csbj.2022.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]  Open
24
Hasegawa K, Moriwaki Y, Terada T, Wei C, Shimizu K. Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides. J Bioinform Comput Biol 2022;20:2250026. [PMID: 36514872 DOI: 10.1142/s0219720022500263] [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: 11/24/2022]
25
Zhang B, Zhao M, Tian J, Lei L, Huang R. Novel antimicrobial agents targeting the Streptococcus mutans biofilms discovery through computer technology. Front Cell Infect Microbiol 2022;12:1065235. [PMID: 36530419 PMCID: PMC9751416 DOI: 10.3389/fcimb.2022.1065235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]  Open
26
Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multiscale profiling of protease activity in cancer. Nat Commun 2022;13:5745. [PMID: 36192379 PMCID: PMC9530178 DOI: 10.1038/s41467-022-32988-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/24/2022] [Indexed: 11/09/2022]  Open
27
Soleymani F, Paquet E, Viktor H, Michalowski W, Spinello D. Protein-protein interaction prediction with deep learning: A comprehensive review. Comput Struct Biotechnol J 2022;20:5316-5341. [PMID: 36212542 PMCID: PMC9520216 DOI: 10.1016/j.csbj.2022.08.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022]  Open
28
Villalobos-Alva J, Ochoa-Toledo L, Villalobos-Alva MJ, Aliseda A, Pérez-Escamirosa F, Altamirano-Bustamante NF, Ochoa-Fernández F, Zamora-Solís R, Villalobos-Alva S, Revilla-Monsalve C, Kemper-Valverde N, Altamirano-Bustamante MM. Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field. Front Bioeng Biotechnol 2022;10:788300. [PMID: 35875501 PMCID: PMC9301016 DOI: 10.3389/fbioe.2022.788300] [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] [Received: 10/02/2021] [Accepted: 05/25/2022] [Indexed: 11/23/2022]  Open
29
Zhaxi Y, Xiang Y, Zou J, Zhang F. Exploration of the Educational Utility of National Film Using Deep Learning From the Positive Psychology Perspective. Front Psychol 2022;13:804447. [PMID: 35756315 PMCID: PMC9218536 DOI: 10.3389/fpsyg.2022.804447] [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: 10/29/2021] [Accepted: 05/03/2022] [Indexed: 11/13/2022]  Open
30
Otović E, Njirjak M, Kalafatovic D, Mauša G. Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides. J Chem Inf Model 2022;62:2961-2972. [PMID: 35704881 DOI: 10.1021/acs.jcim.2c00526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Wan F, Kontogiorgos-Heintz D, de la Fuente-Nunez C. Deep generative models for peptide design. DIGITAL DISCOVERY 2022;1:195-208. [PMID: 35769205 PMCID: PMC9189861 DOI: 10.1039/d1dd00024a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/19/2022] [Indexed: 12/13/2022]
32
Assessing sequence-based protein-protein interaction predictors for use in therapeutic peptide engineering. Sci Rep 2022;12:9610. [PMID: 35688894 PMCID: PMC9187631 DOI: 10.1038/s41598-022-13227-9] [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] [Received: 10/01/2021] [Accepted: 04/25/2022] [Indexed: 12/01/2022]  Open
33
Park SO, Jeong H, Park J, Bae J, Choi S. Experimental demonstration of highly reliable dynamic memristor for artificial neuron and neuromorphic computing. Nat Commun 2022;13:2888. [PMID: 35660724 PMCID: PMC9166790 DOI: 10.1038/s41467-022-30539-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/04/2022] [Indexed: 01/08/2023]  Open
34
Kucera T, Togninalli M, Meng-Papaxanthos L. Conditional generative modeling for de novo protein design with hierarchical functions. Bioinformatics 2022;38:3454-3461. [PMID: 35639661 PMCID: PMC9237736 DOI: 10.1093/bioinformatics/btac353] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/20/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022]  Open
35
Jukič M, Bren U. Machine Learning in Antibacterial Drug Design. Front Pharmacol 2022;13:864412. [PMID: 35592425 PMCID: PMC9110924 DOI: 10.3389/fphar.2022.864412] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022]  Open
36
Talluri S. Algorithms for protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022;130:1-38. [PMID: 35534105 DOI: 10.1016/bs.apcsb.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
37
Chen Q, Yang C, Xie Y, Wang Y, Li X, Wang K, Huang J, Yan W. GM-Pep: A High Efficiency Strategy to De Novo Design Functional Peptide Sequences. J Chem Inf Model 2022;62:2617-2629. [PMID: 35533298 DOI: 10.1021/acs.jcim.2c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
38
Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, Zaitzeff A, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E. Large-scale design and refinement of stable proteins using sequence-only models. PLoS One 2022;17:e0265020. [PMID: 35286324 PMCID: PMC8920274 DOI: 10.1371/journal.pone.0265020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/18/2022] [Indexed: 12/25/2022]  Open
39
Novel Antimicrobial Peptides Designed Using a Recurrent Neural Network Reduce Mortality in Experimental Sepsis. Antibiotics (Basel) 2022;11:antibiotics11030411. [PMID: 35326874 PMCID: PMC8944797 DOI: 10.3390/antibiotics11030411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/28/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023]  Open
40
Cesaro A, Torres MDT, de la Fuente-Nunez C. Methods for the design and characterization of peptide antibiotics. Methods Enzymol 2022;663:303-326. [PMID: 35168794 DOI: 10.1016/bs.mie.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
41
Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022;13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022]  Open
42
Hamre J, Jafri MS. Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. INFORMATICS IN MEDICINE UNLOCKED 2022;29:100886. [PMID: 35252541 PMCID: PMC8883729 DOI: 10.1016/j.imu.2022.100886] [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] [Received: 12/23/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 11/30/2022]  Open
43
Thomas S, Abraham A, Baldwin J, Piplani S, Petrovsky N. Artificial Intelligence in Vaccine and Drug Design. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2410:131-146. [PMID: 34914045 DOI: 10.1007/978-1-0716-1884-4_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
44
Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022;14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]  Open
45
Greener JG, Kandathil SM, Moffat L, Jones DT. A guide to machine learning for biologists. Nat Rev Mol Cell Biol 2022;23:40-55. [PMID: 34518686 DOI: 10.1038/s41580-021-00407-0] [Citation(s) in RCA: 470] [Impact Index Per Article: 235.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
46
Rudden LSP, Hijazi M, Barth P. Deep learning approaches for conformational flexibility and switching properties in protein design. Front Mol Biosci 2022;9:928534. [PMID: 36032687 PMCID: PMC9399439 DOI: 10.3389/fmolb.2022.928534] [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: 04/25/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]  Open
47
Dong Y, Zhang Y, Liu F, Cheng X. Reservoir Production Prediction Model Based on a Stacked LSTM Network and Transfer Learning. ACS OMEGA 2021;6:34700-34711. [PMID: 34963953 PMCID: PMC8697399 DOI: 10.1021/acsomega.1c05132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/25/2021] [Indexed: 05/24/2023]
48
Dean SN, Alvarez JAE, Zabetakis D, Walper SA, Malanoski AP. PepVAE: Variational Autoencoder Framework for Antimicrobial Peptide Generation and Activity Prediction. Front Microbiol 2021;12:725727. [PMID: 34659152 PMCID: PMC8515052 DOI: 10.3389/fmicb.2021.725727] [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: 06/15/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022]  Open
49
Melo MCR, Maasch JRMA, de la Fuente-Nunez C. Accelerating antibiotic discovery through artificial intelligence. Commun Biol 2021;4:1050. [PMID: 34504303 PMCID: PMC8429579 DOI: 10.1038/s42003-021-02586-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023]  Open
50
Heinen S, von Rudorff GF, von Lilienfeld OA. Toward the design of chemical reactions: Machine learning barriers of competing mechanisms in reactant space. J Chem Phys 2021;155:064105. [PMID: 34391351 DOI: 10.1063/5.0059742] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
PrevPage 1 of 3 123Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA