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In Silico De Novo Synthesis, Screening, and ADME/T Profiling of dna-pA104R Inhibitors as Potential African Swine Fever therapeutics

In Silico De Novo Synthesis, Screening, and ADME/T Profiling...

引用

15th international Joint conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2022

作者： Reyes, Kim Rafaelle E. Roxas, Timothy Jen R. Gomez, Marineil Tayo, Lemmuel L. School of Chemical Biological and Materials Engineering and Sciences Mapúa University 658 Muralla Street Intramuros Manila Philippines

African Swine Fever Virus (ASFV) is a dsdna virus causative of the African Swine Fever (ASF) in wild and domestic hogs. ASF is characterized by hemorrhagic fever, high mortality, and transmissibility. the binding of the dna to the pA104R protein mediates viral replication and genome packaging. In the present study, we generated nine (9) reference compounds that exhibited high docking affinities through de novo computer aided drug design (CADD). these compounds were then used as query molecules to find commercially available drug-like compounds using ligand-based virtual screening (VS). We were able to retrieve 900 hit compounds that exhibited the same pharmacophoric activities. then, these hit compounds were subjected to drug-likeness filtration to identify the most likely to be developed as commercial drugs based on established parameters. We identified sixty-two (62) drug-like molecules. molecular docking was then performed to determine the top five compounds with the highest binding affinities against the target protein. ADME/T profiling was done on these compounds to assess their pharmacokinetic properties. Compound 8.45 performed best based on our devised scoring system. this paper shall serve as a good reference in the discovery and development of anti-ASFV therapeutics. © 2022 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved.

关键词： molecular docking

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Finding a disease-related gene from microarray data using random forest

Finding a disease-related gene from microarray data using ra...

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IEEE international conference on Cognitive Informatics

作者： Kazutaka Nishiwaki Katsutoshi Kanamori Hayato Ohwada Department of Industrial Administration Tokyo University of Science Chiba Japan

ISBN: (纸本)9781509038473

Numerous databases of dna-microarrays are now widely available on the internet. Recently, there has been increasing interest in the analysis of microarray data using machine-learning techniques due to the amount of data, which is too massive for researchers to analyze using conventional techniques. In this study, we propose a method of finding a disease-related gene from microarray data using random forest, a machine-learning technique. More specifically, we focused on Alzheimer's disease and used microarray data related to Alzheimer's disease in the experiments. In the result, we found some genes that are believed to be related to Alzheimer's disease. Some genes discovered in the result have been investigated for their relevance to Alzheimer's disease, and this proves that our proposed methodology was successful in finding disease-related genes using microarray data. In addition, the proposed methodology is useful in providing new knowledge for biologists, medical scientists, and cognitive computing researchers since there is no previous work on genes that focused on finding a disease-related gene for Alzheimer's disease.

关键词： Gene expression Alzheimer's disease dna Support vector machines Decision support systems Internet

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A Multiagent System for the Analysis of Sequence Data

A Multiagent System for the Analysis of Sequence Data

引用

international conference on Information Fusion

作者： Roberto González Juan F. De Paz Carolina Zato Javier Bajo Gabriel Villarubia Juan M. Corchado Computer Science University of Salamanca Salamanca (Spain)

ISBN: (纸本)9781467304177

the analysis of sequence data requires the processing of the data obtained from sequencers for their subsequent comparison with genomes. the information recovered from the sequencers must be assembled and aligned in order to recover the variations that exist in the patient dna. this study proposes a system to detect and classify variations by integrating information taken from biomedical databases. the system incorporates different algorithms to search for differences as compared to the reference genome for patients.

关键词： component genetic sequencing distributed computing bioinformatics

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Algorithms for the typing of related dna sequences

Algorithms for the typing of related DNA sequences

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international conference on Electronics, Communications and Computers (CONIELECOMP)

作者： R.S. Rodriguez C.Y.C. Roldan J.G. Eisele P.G. Gil M.J.O. Galindo Department of Computer Science Universidad de las Américas-Puebla Puebla Mexico Department of Chemistry and Biology Universidad de las Américas-Puebla Puebla Mexico

this article presents an approach to solve the typing problem using algorithms for set covering. Two algorithms to solve this problem were designed and compared. the typing problem consists of distinguishing all sequences using the least possible reagents. For each reagent, their capacity to distinguish between pairs of sequences is represented in a matrix and-then mapped to the set-covering problem. In (J. Lozano Yecora, MS thesis. Uni. de las Americas, Puebla, Dept. of Comp. Science, 2004), a proof of the equivalence of this problem with the set covering problem is presented; here, the results of an exact algorithm to solve the set-covering problem are presented. this algorithm uses a branch and bound method based on some intuitive properties of the solution, applying recursion as the final resource. Two approximation algorithms were also implemented and tested. One is an improved greedy algorithm and the other is based on dynamic programming. Real as well as randomly created instances were used to test the algorithms.

关键词： dna Sequences Biochemistry Testing Probes Logic programming Gas insulated transmission lines Computer science Chemistry Biology

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Families of FPGA-based algorithms for approximate string matching

Families of FPGA-based algorithms for approximate string mat...

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international conference on Application Specific Systems (ASAP), Architectures and Processors

作者： T. Van Court M.C. Herbordt ECE Department Boston University USA

Dynamic programming for approximate string matching is a large family of different algorithms, which vary significantly in purpose, complexity, and hardware utilization. Many implementations have reported impressive speed-ups, but have typically been point solutions -highly specialized and addressing only one or a few of the many possible options. the problem to be solved is creating a hardware description that implements a broad range of behavioral options without losing efficiency due to feature bloat. We report a set of three component types that address different parts of the DP string matching problem. Multiple, interchangeable implementations are available for each component type. this allows each application to choose the feature set required, then make maximum use of the FPGA fabric according to that application's specific resource requirements. Synthesis estimates show a 4:1 improvement in time-space performance, depending on the options chosen for a specific matching task.

关键词： Hardware Dynamic programming Bioinformatics Sequences Field programmable gate arrays Fabrics Databases dna Proteins Amino acids

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A survey of cyber crime in India

A survey of cyber crime in India

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international conference on Advanced computing Technologies (ICACT)

作者： Vinit Kumar Gunjan Amit Kumar Sharda Avdhanam TATA Consultancy Services Ltd Hyderabad Andhra Pradesh India BioAxis DNA Research Centre Pvt Ltd Hyderabad Andhra Pradesh India A P Police Academy Hyderabad Andhra Pradesh India

Cybercrime is all about the crimes in which communication channel and communication device has been used directly or indirectly as a medium whether it is a Laptop, Desktop, PDA, Mobile phones, Watches, Vehicles. the report titled “Global Risks for 2012”, predicts cyber-attacks as one of the top five risks in the World for Government and business sector. Cyber crime is a crime which is harder to detect and hardest to stop once occurred causing a long term negative impact on victims. With the increasing popularity of online banking, online shopping which requires sensitive personal and financial data, it is a term that we hear in the news with some frequency. Now, in order to protect ourselves from this crime we need to know what it is and how it does works against us. this paper presents a brief overview of all about cyber criminals and crime with its evolution, types, case study, preventive majors and the department working to combat this crime.

关键词： Computers Electronic mail Computer crime Internet Banking IP networks

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international conference on Application Specific Systems (ASAP), Architectures and Processors

作者： P. Krishnamurthy J. Buhler R. Chamberlain M. Franklin M. Gyang J. Lancaster Department of Computer Science and Engineering Washington University Saint Louis USA

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. the most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches dna sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.

关键词： Sequences Hardware Databases Application software dna Genomics Bioinformatics Computer architecture Read-write memory Evolution (biology)

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Antigenic epitope prediction of small envelope protein and designing a vaccine by using reverse vaccinology approach against SARS coronavirus Tor2 strain

Antigenic epitope prediction of small envelope protein and d...

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international conference on Advanced computing Technologies (ICACT)

作者： Amit Kumar Anupam Bhattacharya Amita Kashyap BioAxis DNA Research Centre (P) Ltd Hyderabad India

Severe acute respiratory syndrome (SARS) is a serious form of pneumonia which results in acute respiratory distress and sometimes death. In this study, we applied the reverse vaccinology approach to determine the antigenic determinant sites present on the protein. the method incorporates the prediction of antigenic sites, solvent accessible region and secondary structure, B-cell epitope prediction, and the designing of antigenic determinant. the results of the study suggested that small envelope protein and orf8 protein could be potential candidates for vaccine designing. the high scoring antigenic peptides were designed and optimized. It is inferred that peptide of small envelope protein will make a very stable and effective vaccine targeting the E protein of the virus which is responsible for the spread of the virion. this study provides a strong and a potential optimized vaccine against SARS, which has high chances of success of immunization and higher probabilities of combating the dreadful disease.

关键词： Proteins Vaccines Peptides Bioinformatics Databases Genomics Viruses (medical)

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Biclustering Expression Data Using Node Addition Algorithm

Biclustering Expression Data Using Node Addition Algorithm

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international conference on Advanced computing and Communications (ADCOM)

作者： B. Borah D.K. Bhattacharyya Department of Computer Science and Engineering Tezpur University Tezpur India

Biclustering algorithms simultaneously cluster both rows and columns. this type of algorithms are applied to gene expression data analysis to find a subset of genes that exhibit similar expression pattern under a subset of conditions. Cheng and Church introduced the mean squared residue measure to capture the coherence of a subset of genes over a subset of conditions. they provided a set of heuristic algorithms based primarily on node deletion to find one bicluster or a set of biclusters after masking discovered biclusters with random values. Masking of discovered biclusters with random values interferes with discovery of high quality biclusters. We provide an efficient node addition algorithm to find a set of biclusters without the need of masking discovered biclusters. Initialized with a gene and a subset of conditions, a bicluster is extended by adding more genes and conditions. thus it provides facility to study individual genes, besides generating a large number of biclusters with different initializations. Biclusters with lower or higher scores within a specified limit can be generated by parameter setting. Use of incremental method of computing score makes the algorithm faster.

关键词： Gene expression Clustering algorithms Data analysis Heuristic algorithms Biology computing Fluctuations Computer science Data engineering Coherence dna

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Back Translated Peptide K-mer Search and Local Alignment in Large dna Sequence Databases Using BoND-SD-tree Indexing

Back Translated Peptide K-mer Search and Local Alignment in ...

引用

IEEE international conference on Bioinformatics and Bioengineering

作者： AKM Tauhidul Islam Sakti Pramanik Xinge Ji James R. Cole Qiang Zhu Michigan State University University of Michigan

ISBN: (纸本)9781467379847

In the past, genome sequence databases had used main memory indexing, such as the suffix tree, for fast sequence searches. With next generation sequencing technologies, the amount of sequence data being generated is huge and main memory indexing is limited by the amount of memory available. K-mer based techniques are being more used for various genome sequence database applications such as local alignment. K-mer can also provide an excellent basis for creating efficient disk based indexing. In this paper, we have proposed a k-mer based database searching and local alignment tool using box queries on BoND-SD-tree indexing. BoND-tree is quite efficient for indexing and searching in Non-Ordered Discrete Data Space (NDDS). We have conducted experiments on searching dna sequence databases using back translated protein query sequences and have compared with existing methods. We have also implemented local alignment of back translated protein query sequences with large dna sequence databases using this index based k-mer search. Performances of this local alignment approach have been compared with that of Tblastn of NCBI. the results are quite promising and justify significance of the proposed approach.

关键词： dna Sequence Databases Indexing alignment tool Database searching molecular Sequence Data

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