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In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials [article]

Ho-min Park, Yunseol Park, Urta Berani, Eunkyu Bang, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve, Hyunjin Shim
2022 bioRxiv   pre-print
Next, we test a number of RNA-protein interaction programs to optimize the in silico docking of crRNAs with the Cas13 proteins.  ...  From this optimized pipeline, we find a number of candidate crRNAs that have comparable or better in silico docking with the Cas13 proteins of the current tools.  ...  Acknowledgements The research and development activities described in this study were funded by Ghent University Global Campus (GUGC), Incheon, Korea.  ... 
doi:10.1101/2022.06.21.496952 fatcat:nod3ogvlqnh2vemgzmvv6splku

Computational Drug Design and Molecular Dynamic Studies-A Review

Maithri G, Manasa B, Vani SS, Narendra A, Harshita T
2017 International Journal of Biomedical Data Mining  
Therefore in-silico methods have been of great importance in target identification and in prediction of novel drugs.  ...  Drug designing using in-silico methods is cost effective in research and development of drugs. Currently, a vast number of software's used in drug design.  ...  The use in silico methods will help us in all aspects of drug discovery today and forms the importance of structure-based drug design.  ... 
doi:10.4172/2090-4924.1000123 fatcat:muzpq5eunfhs5flkdkxnq5e7ca

Interaction of Enzyme-Substrate from Indigenous Cellulolytic Bacteria by Bioinformatics

Yanty Maryanty, Tri adryati, Suharjono, Sutiman Bambang Sumitro
2020 IOP Conference Series: Materials Science and Engineering  
While the results of the analysis based on isolation of cellulase encoding genes from isolate B were predicted in-silico showed the interaction between hydrogen bonds in tyrosin (TRY 299), glutamine (GLU201  ...  Isolate B predicted that its homology in silico can degrade cellulose substrate with the binding affinity of -7.0 Kcal/mol while based on the results of isolation of cellulase encoding genes shows the  ...  In this method, the structure of the target protein is determined based on other proteins namely the insolate protein that has been recognized by its tertiary structure.  ... 
doi:10.1088/1757-899x/854/1/012068 fatcat:b7iw43a6mnas3m2lijay4tskdq

In silico target identification of biologically active compounds using an inverse docking simulation

Youngjin Choi
2013 TANG [HUMANITAS MEDICINE]  
The aim of this review is to introduce a series of in silico works for predicting potential drug targets and side-effects based on inverse docking simulations.  ...  Inverse docking simulation is a reverse use of molecular docking involving multiple target searches for known chemical structure.  ...  ACKNOWLEDGEMENTS This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2010-0004820  ... 
doi:10.5667/tang.2013.0008 fatcat:obc2k7q4ibg53ji3l76fvfz6ha

IN SILICO STUDY OF Stachytarpheta jamaicensis ACTIVE COMPOUNDS AS ANTIBACTERIAL MATERIAL

Juliyatin Putri Utami, Sherli Diana, Rahmad Arifin
2022 Dentino Jurnal Kedokteran Gigi  
Objective: This study aims to evaluate the interaction of active compound S. jamaecensis with bacterial proteins through an in silico study.  ...  One of the first steps in predicting the effectiveness of these compounds can be done through in-Silico studies with molecular docking.  ...  This study aims to evaluate the interaction of the active compound S. jamaicensis with bacterial proteins through in silico research.  ... 
doi:10.20527/dentino.v7i1.13105 fatcat:b74q2vh2vra4ffzcgndzpanlq4

In silico protein engineering: Methods and Tools [chapter]

Sneha Thomas, John J. Georrge
2018 Zenodo  
It is based on altering the affinity of a protein by replacing some amino-acid residues to identify the essential residues and their specific involvement in the binding activity.  ...  Protein engineering strategies aimed at constructing enzymes with novel or improved activities, specificity, and stabilities greatly benefit from in silico methods such as (i) bioinformatics, (ii) molecular  ...  STEPS OF PROTEIN ENGINEERING The first describes methods for 3D structure prediction, a necessary step to perform in silico engineering but not involved in the engineering itself.  ... 
doi:10.5281/zenodo.4729854 fatcat:a6ah2mwsgnfdvd7ybni6igltp4

In silico elucidation of potential drug target sites of the Thumb Index Fold Protein, Wnt-8b

Sheikh Arslan Sehgal, Sonia Kanwal, Rana Adnan Tahir, Zunera Khalid, Mirza A. Hammad
2018 Tropical Journal of Pharmaceutical Research  
Methods: Threading and comparative modeling approaches were employed to predict the 3D structure of Wnt-8b.  ...  Literature-derived compounds were selected for comparative molecular docking studies using GOLD, AutoDock and AutoDock Vina.  ...  Acknowledgement The authors acknowledge Mr Tassaduq Hussain Jaffer, Bioinformatics Research Laboratory, Department of Biosciences, CIIT Sahiwal, for his support throughout the manuscript.  ... 
doi:10.4314/tjpr.v17i3.15 fatcat:ouahbxn6cbb73pg2mf5wjspv3q

In Silico evaluation and identification of fungi capable of producing endo-inulinase enzyme

Jayaram Chikkerur, Ashis Kumar Samanta, Arindam Dhali, Atul Purushottam Kolte, Sohini Roy, Pratheepa Maria, Maureen J. Donlin
2018 PLoS ONE  
This study aimed to identify the fungi capable of producing endo-inulinase based on the in silico analysis of proteins retrieved from non-redundant protein sequence database.  ...  The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1371/journal.pone.0200607 pmid:30001376 pmcid:PMC6042768 fatcat:hhleiax24bcnhjpewjsbmbsgqe

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
Key words: virtual ligand screening, structure-based drug design, docking, scoring, drug discovery, protein-protein interaction.  ...  A wide range of "in silico methods" can be used to facilitate the design of protein-protein modulators.  ...  This approach is sometimes misleading and several authors have proposed to evaluate the presence of key interactions between the docked ligands and the protein versus the ones present in the crystal structure  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

In silico Techniques for Prospecting and Characterizing Monoclonal Antibodies [chapter]

Tania M. Manieri, Carolina G. Magalhaes, Daniela Y. Takata, João V. Batalha-Carvalho, Ana M. Moro
2020 Monoclonal Antibodies [Working Title]  
In silico methods, such as homology modeling, to predict antibody structures, identification of epitope-paratope interactions, and molecular docking are useful to generate 3D structures of the antibody–antigen  ...  Algorithms and software set the in silico techniques on the innovation frontier.  ...  Molecular docking tools (Table 1 ) allow predicting the best binding interface of two interacting proteins.  ... 
doi:10.5772/intechopen.94366 fatcat:7tt2sdxmfbcjrkdoobllr6viuu

In silico Evaluation of Solanine Compound as New Potential Inhibitors of Cancer Causing Enzymes

Rajalakshmi A, Jayachitra A
2021 Acta Scientific Pharmaceutical Sciences  
Explore the interaction mode and binding orientation of lead compound with target proteins by molecular docking studies and understand the structural insights and functional properties of potent target  ...  Aim of this study to analyze the interaction of Solanine with cancer causing enzymes.  ...  The protein and ligand interaction plays a significant role in structural based designing.  ... 
doi:10.31080/asps.2021.05.0805 fatcat:xng3dlfjtzg6ldqxx2lte4kjne

In silico prediction of telomerase reverse transcriptase inhibitors using modified retinol for the treatment of arsenical cancer

Kipchu Tshering, Mir Misbahuddin
2016 Bangabandhu Sheikh Mujib Medical University Journal  
<p align="left">Retinol molecule was modified to predict the inhibitors of telomerase reverse transcriptase for the treatment of arsenical cancer through in silico study.  ...  The inhibitors were predicted through molecular docking of modified retinol with telomerase reverse transcriptase.  ...  Identification of such a molecule can be predicted from molecular docking since docking process is used to understand the drug-receptor interaction and now-a-days plays an important role in modern drug  ... 
doi:10.3329/bsmmuj.v9i3.29650 fatcat:3mvv2ng7srg5fh3bbccznrbg2i

In silico evidence of de novo interactions between ribosomal and Epstein - Barr virus proteins

Edmund Ui-Hang Sim, Shruti Prashant Talwar
2019 BMC Molecular and Cell Biology  
Association of Epstein-Barr virus (EBV) encoded latent gene products with host ribosomal proteins (RPs) has not been fully explored, despite their involvement in the aetiology of several human cancers.  ...  To gain an insight into their plausible interactions, we employed a computational approach that encompasses structural alignment, gene ontology analysis, pathway analysis, and molecular docking.  ...  Conclusion Based on structural similarity-based prediction protocol, we have provided in silico evidence of 48 de novo biologically relevant protein-protein interactions among 27 ribosomal proteins and  ... 
doi:10.1186/s12860-019-0219-y pmid:31416416 pmcid:PMC6694676 fatcat:n5nlkqre6bf3pfkvxxrnkk4k4a

In Silico Study to Develop a Lectin-Like Protein from Mushroom Agaricus bisporus for Pharmaceutical Application

Wangsa Tirta ISMAYA
2016 Scientia Pharmaceutica  
As the characteristics of LSMT are unknown, a structural study in silico was performed to assess its potential pharmaceutical application.  ...  .: Sci Pharm. 2016; 84: 203-217 Keywords In silico protein study • Lectin-like protein • Light subunit mushroom tyrosinase • Molecular docking • Novel pharmaceutical protein • Oral delivery  ...  This binding pocket was recorded and considered in evaluating structural model of LSMT and of its homologs. Based on those results, further structural evaluation was conducted.  ... 
doi:10.3797/scipharm.isp.2015.11 pmid:27110510 pmcid:PMC4839548 fatcat:nx2mkjylsbd4za2pfkj5sronwi

Probing Binding Mechanism of Interleukin-6 and olokizumab: In Silico Design of Potential lead Antibodies for Autoimmune and Inflammatory Diseases

Dibyabhaba Pradhan, Rashi Verma, Monika Yadav, Arun Kumar Jain
2017 Journal of Cell Signaling  
The functionally important binding pockets or protein-protein interacting sites in the tertiary structure of drug targets are the intriguing starting point of structure based drug design.  ...  Therefore, ZDOCK, ClusPro and RosettaDock inspire confidence for being used for antigen-antibody docking/protein-protein docking to predict binding orientations as well as affinities.  ... 
doi:10.4172/2576-1471.1000165 fatcat:5k27svcz4jeu3bwdttwsmt7ryi
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