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ACP-GCN: the identification of anticancer peptides based on Graph Convolution Networks

Bing Rao, Lichao Zhang, Guoying Zhang
2020 IEEE Access  
In this paper, we propose a new graph learning based computational model, named ACP-GCN, to automatically and accurately predict ACPs based on graph convolution networks.  ...  However, most of computational methods make predictions based on machine learning using hand-crafted features.  ...  Anticancer peptides classification based on graph convolutional neural network.  ... 
doi:10.1109/access.2020.3023800 fatcat:okdz5qgrwjfollkuii7ldnv3iu

In Silico Analysis of Epitope-Based Vaccine Candidates against Hepatitis B Virus Polymerase Protein

Juzeng Zheng, Xianfan Lin, Xiuyan Wang, Liyu Zheng, Songsong Lan, Sisi Jin, Zhanfan Ou, Jinming Wu
2017 Viruses  
In this research, a computational approach was employed to predict suitable HBV polymerase targeting multi-peptides for vaccine candidate selection.  ...  Criteria-based analysis provided four predicted epitopes, RVTGGVFLV, VSIPWTHKV, YMDDVVLGA and HLYSHPIIL.  ...  Acknowledgments: We gratefully acknowledge financial support from the Natural Science Foundation of Zhejiang Province (LY12H03003).  ... 
doi:10.3390/v9050112 pmid:28509875 pmcid:PMC5454424 fatcat:opaajzzubjgxbmjix7r5escsmq

Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria

Taimoor Khan, Muhammad Abdullah, Tayyba Fatima Toor, Fahad N. Almajhdi, Muhammad Suleman, Arshad Iqbal, Liaqat Ali, Abbas Khan, Yasir Waheed, Dong-Qing Wei
2022 Frontiers in Medicine  
Further validations based on in silico cloning revealed a CAI score of 0.98 and an optimal percentage of GC contents (54.4%) indicated a putatively higher expression of the vaccine construct in Escherichia  ...  Efforts are needed to design effective therapeutic strategies to curtail the emergence of this bacterium.  ...  The use of computational tools has significantly reduced the cost and time of developing peptides-based therapeutics.  ... 
doi:10.3389/fmed.2021.825876 pmid:35186980 pmcid:PMC8854494 fatcat:ohw2lg3yl5haliy4qysoxjfd2y

Whole Proteome-Based Therapeutic Targets Annotation and Designing of Multi-Epitope-Based Vaccines against the Gram-Negative XDR-Alcaligenes faecalis Bacterium

Metab Alharbi, Abdulrahman Alshammari, Abdullah F. Alasmari, Saud Alharbi, Muhammad Tahir ul Qamar, Sumra Wajid Abbasi, Bilal Shaker, Sajjad Ahmad
2022 Vaccines  
This was followed by targeted protein-specific immune epitope prediction and prioritization.  ...  In the current study, a subtractive proteomics approach was adapted to annotate the whole proteome of Alcaligenes faecalis and prioritize target proteins for vaccine-related therapeutics design.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/vaccines10030462 pmid:35335094 pmcid:PMC8955209 fatcat:bsqzmo7ssfgxlhjbevz34yx6cy

In-silico evaluation of the potential of a viral protein (apoptin) as an anticancer agent

Masoud E. Razliqi, Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran, Ali Najafi, Gholamreaza Olad, Hadi E.G. Ghaleh, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran, Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran, Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
2021 Romanian Journal of Military Medicine  
The results of in-silico analysis indicated that this protein had a stable structure, was a suitable choice for therapeutic goals, capable of acting as a good anti-cancer agent.  ...  Apoptin has attracted much attention because of causes specific death in transformed and cancer cells and has toxic effects on cancer cells.  ...  and analysis of data.  ... 
doi:10.55453/rjmm.2021.124.4.12 fatcat:3hapu3qx6vb2pbnriexivyahru

Molecular characterization of a novel β-defensin isoform from the red-toothed trigger fish, Odonus niger (Ruppel, 1836)

S. Neelima, K. Archana, P. P. Athira, M. V. Anju, V. V. Anooja, I. S. Bright Singh, Rosamma Philip
2021 Journal of Genetic Engineering and Biotechnology  
Antimicrobial peptides (AMPs) with their versatile therapeutic properties are a group of promising molecules with curative potentials.  ...  On-Def was predicted to be non-hemolytic with anti-bacterial, anti-viral, anti-fungal, anti-cancer, and immunomodulatory potential.  ...  Also, there is possibility for oligomeric assembly leading to higher activity/interaction with other immune-related peptides based on higher Boman index predicted.  ... 
doi:10.1186/s43141-021-00175-6 pmid:33978838 fatcat:zthcj5525jerneb347sikvja7i

Computer-aided design of amino acid-based therapeutics: a review

Tayebeh Farhadi, Seyed MohammadReza Hashemian
2018 Drug Design, Development and Therapy  
Most features of computational peptide design are based on the accuracy and efficacy of affinity prediction.  ...  . 117 To predict the protein-peptide binding potency, a number of strict theories were suggested based on the potential free energy perturbation.  ... 
doi:10.2147/dddt.s159767 pmid:29795978 pmcid:PMC5958949 fatcat:mkd3acifezhb3cq2pfdo2ngxb4

Amino Acid Composition and Charge Based Prediction of Antisepsis Peptides by Random Forest Machine Learning Algorithm [article]

AAYUSHI RATHORE, ANU SAINI, NAVJOT KAUR, APARNA SINGH, OJASVI DUTTA, MRINAL BAMHOTRA, AVNEET SAINI, SANDEEP SAINI
2021 bioRxiv   pre-print
Machine learning algorithms are useful in screening and identification of therapeutic peptides and thus provide initial filters or built confidence before using time consuming and laborious experimental  ...  To our knowledge this is the first attempt to build a machine learning classifier for prediction of ASPs.  ...  The use of these tools in the development of peptide-based therapeutics is already revolutionizing protein research by unravelling their novel therapeutic peptide functions [11] .  ... 
doi:10.1101/2021.09.26.461860 fatcat:a5vgl5ld5fc3bdbouyhm3je3em

Graphical representation and mathematical characterization of protein sequences and applications to viral proteins [chapter]

Ambarnil Ghosh, Ashesh Nandy
2011 Advances in Protein Chemistry and Structural Biology  
The emphasis is still on developing the underlying technique, but significant results have been achieved in using these methods for protein phylogeny, mass spectral data of proteins and protein serum profiles  ...  We briefly mention these in this chapter, with some details on protein phylogeny and viral diseases.  ...  An intuitively simpler indexation scheme based on the 20D graphical representation of protein sequences proposed by the present authors ) and described below has been found useful in generating phylogenetic  ... 
doi:10.1016/b978-0-12-381262-9.00001-x pmid:21570664 pmcid:PMC7150266 fatcat:k7jp6wiy3bf3hk4x4m7g45t4oy

Ab initio Designed Antimicrobial Peptides Against Gram-Negative Bacteria

Shravani S. Bobde, Fahad M. Alsaab, Guangshuan Wang, Monique L. Van Hoek
2021 Frontiers in Microbiology  
Laboratory-based experimental results were compared to computationally predicted activities for each of the peptides to ascertain the accuracy of the computational tools used.  ...  Based on our findings, we propose upfront selection of the peptide dataset for analysis, an additional step of positional analysis to add to the ab initio database filtering technology (DFT) method, and  ...  their therapeutic index.  ... 
doi:10.3389/fmicb.2021.715246 pmid:34867843 pmcid:PMC8636942 fatcat:egbamwppmbcvrer24kgde4bw5y

A Vaccine Construction against COVID-19-Associated Mucormycosis Contrived with Immunoinformatics-Based Scavenging of Potential Mucoralean Epitopes

Muhammad Naveed, Urooj Ali, Mohmed Isaqali Karobari, Naveed Ahmed, Roshan Noor Mohamed, Shahabe Saquib Abullais, Mohammed Abdul Kader, Anand Marya, Pietro Messina, Giuseppe Alessandro Scardina
2022 Vaccines  
The vaccine construct, with an antigenicity score of 0.75 covering, on average, 92–98% of the world population, was designed using an immunoinformatics approach.  ...  It elicited a strong predicted innate and adaptive immune response in the form of helper T (Th) cells, cytotoxic T (TC) cells, B cells, natural killer (NK) cells, and macrophages.  ...  Institutional Review Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/vaccines10050664 pmid:35632420 pmcid:PMC9147184 fatcat:uxbqydalsjg5fm7c6lfondje7q

Prediction of Therapeutic Peptides Using Machine Learning: Computational Models, Datasets, and Feature Encodings

Muhammad Attique, Muhammad Shoaib Farooq, Adel Khelifi, Adnan Abid
2020 IEEE Access  
Similarly, the framework model for the computational prediction of the therapeutic peptides has been introduced to characterize the best practices and levels involved in the development of peptide prediction  ...  predict therapeutic peptides.  ...  With the name of PTPD a deep learning based new computational model was proposed to predict therapeutic peptides.  ... 
doi:10.1109/access.2020.3015792 fatcat:3dtsa3w6trhyrc3ej3spdbamle

In Silico identification of angiotensin-converting enzyme inhibitory peptides from MRJP1

Rana Adnan Tahir, Afsheen Bashir, Muhammad Noaman Yousaf, Azka Ahmed, Yasmine Dali, Sanaullah Khan, Sheikh Arslan Sehgal, Ghulam Md Ashraf
2020 PLoS ONE  
AHTpin server based on scoring vector machine of regression models, proteolysis and structural characterization approaches were implemented to identify the potential inhibitory peptides.  ...  The anti-hypertensive peptides were scrutinized based on the QSAR models of anti-hypertensive activity and the molecular docking analyses were performed to explore the binding affinities and potential  ...  The classification models predicted the special type of peptides either AHT or non-AHT based on the descriptors of the training set.  ... 
doi:10.1371/journal.pone.0228265 pmid:32012183 fatcat:zxyjudmbarec5oaof7h2izpnfu

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

Pingping Sun, Haixu Ju, Zhenbang Liu, Qiao Ning, Jian Zhang, Xiaowei Zhao, Yanxin Huang, Zhiqiang Ma, Yuxin Li
2013 Computational and Mathematical Methods in Medicine  
Localizing epitopes by experimental methods is expensive in terms of time, cost, and effort; therefore, computational methods feature for its low cost and high speed was employed to predict B-cell epitopes  ...  In this paper, we review the recent advance of bioinformatics resources and tools in conformational B-cell epitope prediction, including databases, algorithms, web servers, and their applications in solving  ...  PepBank is a database of peptides based on sequential text mining and public peptide data sources [60] .  ... 
doi:10.1155/2013/943636 pmid:23970944 pmcid:PMC3736542 fatcat:52htw2wq2fcg3bnl6f5zndxpde

Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment

Gouri Shankar Pandey, Chen Yanover, Tom E. Howard, Zuben E. Sauna, Morten Nielsen
2013 PLoS Computational Biology  
Next, we compared the affinities computed by NetMHCIIpan, a neural network-based algorithm for MHC-II peptide binding prediction, to the experimentally measured values and concluded that these are in good  ...  The development of neutralizing anti-drug-antibodies to the Factor VIII protein-therapeutic is currently the most significant impediment to the effective management of hemophilia A.  ...  On the other hand, the predictive performance of peptide-MHC-II binding algorithms is, often, not good enough to justify a purely computational approach [18] .  ... 
doi:10.1371/journal.pcbi.1003066 pmid:23696725 pmcid:PMC3656107 fatcat:rf7fovwtdnao3gaklpbq3njyim
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