Publisher: Inderscience Publishers   (Total: 449 journals)

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Showing 1 - 200 of 449 Journals sorted alphabetically
African J. of Accounting, Auditing and Finance     Hybrid Journal   (Followers: 15)
African J. of Economic and Sustainable Development     Hybrid Journal   (Followers: 18)
Afro-Asian J. of Finance and Accounting     Hybrid Journal   (Followers: 9, SJR: 0.195, CiteScore: 0)
American J. of Finance and Accounting     Hybrid Journal   (Followers: 25)
Asian J. of Management Science and Applications     Hybrid Journal   (Followers: 4)
Atoms for Peace: an Intl. J.     Hybrid Journal   (Followers: 3)
Electronic Government, an Intl. J.     Hybrid Journal   (Followers: 18, SJR: 0.424, CiteScore: 1)
EuroMed J. of Management     Hybrid Journal  
European J. of Cross-Cultural Competence and Management     Hybrid Journal   (Followers: 7)
European J. of Industrial Engineering     Hybrid Journal   (Followers: 10, SJR: 0.595, CiteScore: 1)
European J. of Intl. Management     Hybrid Journal   (Followers: 3, SJR: 0.3, CiteScore: 1)
Global Business and Economics Review     Hybrid Journal   (Followers: 3, SJR: 0.154, CiteScore: 0)
Interdisciplinary Environmental Review     Hybrid Journal   (Followers: 3)
Intl. J. of Abrasive Technology     Hybrid Journal   (Followers: 2, SJR: 0.279, CiteScore: 0)
Intl. J. of Accounting and Finance     Hybrid Journal   (Followers: 19)
Intl. J. of Accounting, Auditing and Performance Evaluation     Hybrid Journal   (Followers: 16, SJR: 0.14, CiteScore: 0)
Intl. J. of Ad Hoc and Ubiquitous Computing     Hybrid Journal   (Followers: 8, SJR: 0.21, CiteScore: 1)
Intl. J. of Adaptive and Innovative Systems     Hybrid Journal   (Followers: 1)
Intl. J. of Additive and Subtractive Materials Manufacturing     Hybrid Journal   (Followers: 7)
Intl. J. of Advanced Intelligence Paradigms     Hybrid Journal   (Followers: 5, SJR: 0.144, CiteScore: 1)
Intl. J. of Advanced Mechatronic Systems     Hybrid Journal   (Followers: 3, SJR: 0.132, CiteScore: 0)
Intl. J. of Advanced Media and Communication     Hybrid Journal   (Followers: 27, SJR: 0.124, CiteScore: 0)
Intl. J. of Advanced Operations Management     Hybrid Journal   (Followers: 10, SJR: 0.163, CiteScore: 0)
Intl. J. of Aerodynamics     Hybrid Journal   (Followers: 34)
Intl. J. of Agent-Oriented Software Engineering     Hybrid Journal   (Followers: 3)
Intl. J. of Agile and Extreme Software Development     Hybrid Journal   (Followers: 5)
Intl. J. of Agile Systems and Management     Hybrid Journal   (Followers: 5, SJR: 0.878, CiteScore: 3)
Intl. J. of Agricultural Resources, Governance and Ecology     Hybrid Journal   (Followers: 2, SJR: 0.152, CiteScore: 0)
Intl. J. of Agriculture Innovation, Technology and Globalisation     Hybrid Journal  
Intl. J. of Alternative Propulsion     Hybrid Journal   (Followers: 12)
Intl. J. of Applied Cryptography     Hybrid Journal   (Followers: 9, SJR: 0.455, CiteScore: 3)
Intl. J. of Applied Decision Sciences     Hybrid Journal   (Followers: 1, SJR: 0.275, CiteScore: 1)
Intl. J. of Applied Management Science     Hybrid Journal   (Followers: 4, SJR: 0.229, CiteScore: 0)
Intl. J. of Applied Nonlinear Science     Hybrid Journal   (Followers: 1)
Intl. J. of Applied Pattern Recognition     Hybrid Journal   (Followers: 8)
Intl. J. of Applied Systemic Studies     Hybrid Journal   (SJR: 0.129, CiteScore: 0)
Intl. J. of Arab Culture, Management and Sustainable Development     Hybrid Journal   (Followers: 7)
Intl. J. of Artificial Intelligence and Soft Computing     Hybrid Journal   (Followers: 14)
Intl. J. of Arts and Technology     Hybrid Journal   (Followers: 6, SJR: 0.225, CiteScore: 1)
Intl. J. of Auditing Technology     Hybrid Journal   (Followers: 5)
Intl. J. of Automation and Control     Hybrid Journal   (Followers: 11, SJR: 0.189, CiteScore: 1)
Intl. J. of Automation and Logistics     Hybrid Journal   (Followers: 5)
Intl. J. of Automotive Composites     Hybrid Journal   (Followers: 4)
Intl. J. of Automotive Technology and Management     Hybrid Journal   (Followers: 7, SJR: 0.374, CiteScore: 1)
Intl. J. of Autonomic Computing     Hybrid Journal   (Followers: 2)
Intl. J. of Autonomous and Adaptive Communications Systems     Hybrid Journal   (Followers: 3, SJR: 0.128, CiteScore: 0)
Intl. J. of Aviation Management     Hybrid Journal   (Followers: 7)
Intl. J. of Banking, Accounting and Finance     Hybrid Journal   (Followers: 16, SJR: 0.137, CiteScore: 0)
Intl. J. of Behavioural Accounting and Finance     Hybrid Journal   (Followers: 11)
Intl. J. of Behavioural and Healthcare Research     Hybrid Journal   (Followers: 8)
Intl. J. of Bibliometrics in Business and Management     Hybrid Journal   (Followers: 2)
Intl. J. of Big Data Intelligence     Hybrid Journal   (Followers: 24)
Intl. J. of Big Data Management     Hybrid Journal   (Followers: 2)
Intl. J. of Bio-Inspired Computation     Hybrid Journal   (Followers: 1, SJR: 0.721, CiteScore: 4)
Intl. J. of Bioinformatics Research and Applications     Hybrid Journal   (Followers: 16, SJR: 0.157, CiteScore: 0)
Intl. J. of Biomechatronics and Biomedical Robotics     Hybrid Journal   (Followers: 4)
Intl. J. of Biomedical Engineering and Technology     Hybrid Journal   (Followers: 4, SJR: 0.205, CiteScore: 1)
Intl. J. of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 8)
Intl. J. of Biometrics     Hybrid Journal   (Followers: 5, SJR: 0.155, CiteScore: 0)
Intl. J. of Biotechnology     Hybrid Journal   (Followers: 6, SJR: 0.269, CiteScore: 1)
Intl. J. of Blockchains and Cryptocurrencies     Hybrid Journal   (Followers: 1)
Intl. J. of Bonds and Derivatives     Hybrid Journal   (Followers: 1)
Intl. J. of Business and Data Analytics     Hybrid Journal  
Intl. J. of Business and Emerging Markets     Hybrid Journal   (Followers: 2)
Intl. J. of Business and Globalisation     Hybrid Journal   (Followers: 3, SJR: 0.263, CiteScore: 1)
Intl. J. of Business and Systems Research     Hybrid Journal   (Followers: 1, SJR: 0.104, CiteScore: 0)
Intl. J. of Business Competition and Growth     Hybrid Journal   (Followers: 5)
Intl. J. of Business Continuity and Risk Management     Hybrid Journal   (Followers: 16)
Intl. J. of Business Environment     Hybrid Journal   (Followers: 3)
Intl. J. of Business Excellence     Hybrid Journal   (Followers: 4, SJR: 0.274, CiteScore: 1)
Intl. J. of Business Forecasting and Marketing Intelligence     Hybrid Journal   (Followers: 6)
Intl. J. of Business Governance and Ethics     Hybrid Journal   (Followers: 7, SJR: 0.171, CiteScore: 0)
Intl. J. of Business Information Systems     Hybrid Journal   (Followers: 17, SJR: 0.266, CiteScore: 1)
Intl. J. of Business Innovation and Research     Hybrid Journal   (Followers: 11, SJR: 0.28, CiteScore: 1)
Intl. J. of Business Intelligence and Data Mining     Hybrid Journal   (Followers: 30, SJR: 0.249, CiteScore: 2)
Intl. J. of Business Intelligence and Systems Engineering     Hybrid Journal  
Intl. J. of Business Performance and Supply Chain Modelling     Hybrid Journal   (Followers: 19, SJR: 0.18, CiteScore: 0)
Intl. J. of Business Performance Management     Hybrid Journal   (Followers: 9, SJR: 0.197, CiteScore: 1)
Intl. J. of Business Process Integration and Management     Hybrid Journal   (Followers: 12, SJR: 0.149, CiteScore: 1)
Intl. J. of Chinese Culture and Management     Hybrid Journal   (Followers: 4)
Intl. J. of Circuits and Architecture Design     Hybrid Journal   (Followers: 6)
Intl. J. of Cloud Computing     Hybrid Journal   (Followers: 25)
Intl. J. of Cognitive Biometrics     Hybrid Journal   (Followers: 3)
Intl. J. of Cognitive Performance Support     Hybrid Journal   (Followers: 4)
Intl. J. of Collaborative Engineering     Hybrid Journal   (Followers: 1)
Intl. J. of Collaborative Enterprise     Hybrid Journal   (Followers: 1)
Intl. J. of Collaborative Intelligence     Hybrid Journal   (Followers: 3)
Intl. J. of Communication Networks and Distributed Systems     Hybrid Journal   (Followers: 7, SJR: 0.177, CiteScore: 1)
Intl. J. of Comparative Management     Hybrid Journal  
Intl. J. of Competitiveness     Hybrid Journal   (Followers: 3)
Intl. J. of Complexity in Applied Science and Technology     Hybrid Journal  
Intl. J. of Complexity in Leadership and Management     Hybrid Journal   (Followers: 29)
Intl. J. of Computational Biology and Drug Design     Hybrid Journal   (Followers: 1, SJR: 0.231, CiteScore: 1)
Intl. J. of Computational Complexity and Intelligent Algorithms     Hybrid Journal   (Followers: 2)
Intl. J. of Computational Economics and Econometrics     Hybrid Journal   (Followers: 6)
Intl. J. of Computational Intelligence in Bioinformatics and Systems Biology     Hybrid Journal   (Followers: 13)
Intl. J. of Computational Intelligence Studies     Hybrid Journal   (Followers: 3)
Intl. J. of Computational Materials Science and Surface Engineering     Hybrid Journal   (Followers: 6, SJR: 0.135, CiteScore: 0)
Intl. J. of Computational Medicine and Healthcare     Hybrid Journal   (Followers: 1)
Intl. J. of Computational Science and Engineering     Hybrid Journal   (Followers: 2, SJR: 0.373, CiteScore: 1)
Intl. J. of Computational Systems Engineering     Hybrid Journal   (Followers: 2)
Intl. J. of Computational Vision and Robotics     Hybrid Journal   (Followers: 5, SJR: 0.129, CiteScore: 0)
Intl. J. of Computer Aided Engineering and Technology     Hybrid Journal   (Followers: 3, SJR: 0.131, CiteScore: 0)
Intl. J. of Computer Applications in Technology     Hybrid Journal   (Followers: 1, SJR: 0.225, CiteScore: 1)
Intl. J. of Computers in Healthcare     Hybrid Journal   (Followers: 3)
Intl. J. of Computing Science and Mathematics     Hybrid Journal   (Followers: 2, SJR: 0.299, CiteScore: 1)
Intl. J. of Continuing Engineering Education and Life-Long Learning     Hybrid Journal   (Followers: 5, SJR: 0.196, CiteScore: 0)
Intl. J. of Convergence Computing     Hybrid Journal   (Followers: 2)
Intl. J. of Corporate Governance     Hybrid Journal   (Followers: 5)
Intl. J. of Corporate Strategy and Social Responsibility     Hybrid Journal   (Followers: 6)
Intl. J. of Creative Computing     Hybrid Journal   (Followers: 1)
Intl. J. of Critical Accounting     Hybrid Journal   (Followers: 3)
Intl. J. of Critical Computer-Based Systems     Hybrid Journal   (Followers: 1, SJR: 0.127, CiteScore: 0)
Intl. J. of Critical Infrastructures     Hybrid Journal   (Followers: 2, SJR: 0.173, CiteScore: 1)
Intl. J. of Data Analysis Techniques and Strategies     Hybrid Journal   (Followers: 17, SJR: 0.23, CiteScore: 0)
Intl. J. of Data Mining and Bioinformatics     Hybrid Journal   (Followers: 18, SJR: 0.217, CiteScore: 1)
Intl. J. of Data Mining, Modelling and Management     Hybrid Journal   (Followers: 14, SJR: 0.209, CiteScore: 0)
Intl. J. of Data Science     Hybrid Journal   (Followers: 10)
Intl. J. of Decision Sciences, Risk and Management     Hybrid Journal   (Followers: 10)
Intl. J. of Decision Support Systems     Hybrid Journal   (Followers: 2)
Intl. J. of Design Engineering     Hybrid Journal   (Followers: 11)
Intl. J. of Digital Culture and Electronic Tourism     Hybrid Journal   (Followers: 6)
Intl. J. of Digital Enterprise Technology     Hybrid Journal   (Followers: 1)
Intl. J. of Digital Signals and Smart Systems     Hybrid Journal   (Followers: 2)
Intl. J. of Diplomacy and Economy     Hybrid Journal   (Followers: 7)
Intl. J. of Dynamical Systems and Differential Equations     Hybrid Journal   (Followers: 1, SJR: 0.184, CiteScore: 0)
Intl. J. of Earthquake and Impact Engineering     Hybrid Journal   (Followers: 4)
Intl. J. of Economic Policy in Emerging Economies     Hybrid Journal   (Followers: 4, SJR: 0.134, CiteScore: 1)
Intl. J. of Economics and Accounting     Hybrid Journal   (Followers: 1)
Intl. J. of Economics and Business Research     Hybrid Journal   (Followers: 5, SJR: 0.129, CiteScore: 0)
Intl. J. of Education Economics and Development     Hybrid Journal   (Followers: 6, SJR: 0.156, CiteScore: 0)
Intl. J. of Electric and Hybrid Vehicles     Hybrid Journal   (Followers: 11, SJR: 0.225, CiteScore: 1)
Intl. J. of Electronic Banking     Hybrid Journal   (Followers: 6)
Intl. J. of Electronic Business     Hybrid Journal   (Followers: 2, SJR: 0.24, CiteScore: 0)
Intl. J. of Electronic Customer Relationship Management     Hybrid Journal   (Followers: 3, SJR: 0.148, CiteScore: 0)
Intl. J. of Electronic Democracy     Hybrid Journal   (Followers: 2)
Intl. J. of Electronic Finance     Hybrid Journal   (Followers: 5, SJR: 0.155, CiteScore: 0)
Intl. J. of Electronic Governance     Hybrid Journal   (SJR: 0.142, CiteScore: 1)
Intl. J. of Electronic Healthcare     Hybrid Journal   (Followers: 2, SJR: 0.254, CiteScore: 1)
Intl. J. of Electronic Marketing and Retailing     Hybrid Journal   (Followers: 7, SJR: 0.249, CiteScore: 1)
Intl. J. of Electronic Security and Digital Forensics     Hybrid Journal   (Followers: 8, SJR: 0.137, CiteScore: 0)
Intl. J. of Electronic Transport     Hybrid Journal   (Followers: 9)
Intl. J. of Embedded Systems     Hybrid Journal   (Followers: 6, SJR: 0.48, CiteScore: 1)
Intl. J. of Emergency Management     Hybrid Journal   (Followers: 12, SJR: 0.185, CiteScore: 0)
Intl. J. of Energy Technology and Policy     Hybrid Journal   (Followers: 7, SJR: 0.224, CiteScore: 0)
Intl. J. of Engineering Management and Economics     Hybrid Journal   (Followers: 4)
Intl. J. of Engineering Systems Modelling and Simulation     Hybrid Journal   (Followers: 8, SJR: 0.175, CiteScore: 0)
Intl. J. of Enterprise Network Management     Hybrid Journal   (SJR: 0.118, CiteScore: 0)
Intl. J. of Entertainment Technology and Management     Hybrid Journal   (Followers: 1)
Intl. J. of Entrepreneurial Venturing     Hybrid Journal   (Followers: 1, SJR: 0.308, CiteScore: 1)
Intl. J. of Entrepreneurship and Innovation Management     Hybrid Journal   (Followers: 29, SJR: 0.255, CiteScore: 1)
Intl. J. of Entrepreneurship and Small Business     Hybrid Journal   (Followers: 32, SJR: 0.401, CiteScore: 1)
Intl. J. of Environment and Health     Hybrid Journal   (Followers: 5, SJR: 0.181, CiteScore: 0)
Intl. J. of Environment and Pollution     Hybrid Journal   (Followers: 2, SJR: 0.215, CiteScore: 1)
Intl. J. of Environment and Sustainable Development     Hybrid Journal   (Followers: 17, SJR: 0.132, CiteScore: 0)
Intl. J. of Environment and Waste Management     Hybrid Journal   (Followers: 4, SJR: 0.175, CiteScore: 0)
Intl. J. of Environment, Workplace and Employment     Hybrid Journal   (Followers: 7, SJR: 0.117, CiteScore: 0)
Intl. J. of Environmental Engineering     Hybrid Journal   (Followers: 6)
Intl. J. of Environmental Policy and Decision Making     Hybrid Journal   (Followers: 2)
Intl. J. of Environmental Technology and Management     Hybrid Journal   (Followers: 1, SJR: 0.141, CiteScore: 0)
Intl. J. of Exergy     Hybrid Journal   (Followers: 3, SJR: 0.396, CiteScore: 1)
Intl. J. of Experimental and Computational Biomechanics     Hybrid Journal   (Followers: 8)
Intl. J. of Experimental Design and Process Optimisation     Hybrid Journal   (Followers: 7)
Intl. J. of Export Marketing     Hybrid Journal   (Followers: 3)
Intl. J. of Financial Engineering and Risk Management     Hybrid Journal   (Followers: 5)
Intl. J. of Financial Innovation in Banking     Hybrid Journal   (Followers: 4)
Intl. J. of Financial Markets and Derivatives     Hybrid Journal   (Followers: 5)
Intl. J. of Financial Services Management     Hybrid Journal   (Followers: 1)
Intl. J. of Food Safety, Nutrition and Public Health     Hybrid Journal   (Followers: 22)
Intl. J. of Forensic Engineering     Hybrid Journal   (Followers: 3)
Intl. J. of Forensic Engineering and Management     Hybrid Journal   (Followers: 3)
Intl. J. of Forensic Software Engineering     Hybrid Journal   (Followers: 3)
Intl. J. of Foresight and Innovation Policy     Hybrid Journal   (Followers: 6, SJR: 0.115, CiteScore: 0)
Intl. J. of Functional Informatics and Personalised Medicine     Hybrid Journal   (Followers: 4)
Intl. J. of Fuzzy Computation and Modelling     Hybrid Journal   (Followers: 2)
Intl. J. of Gender Studies in Developing Societies     Hybrid Journal   (Followers: 6)
Intl. J. of Global Energy Issues     Hybrid Journal   (Followers: 8, SJR: 0.199, CiteScore: 0)
Intl. J. of Global Environmental Issues     Hybrid Journal   (Followers: 3, SJR: 0.153, CiteScore: 0)
Intl. J. of Global Warming     Hybrid Journal   (Followers: 2, SJR: 0.259, CiteScore: 1)
Intl. J. of Globalisation and Small Business     Hybrid Journal   (Followers: 14, SJR: 0.233, CiteScore: 1)
Intl. J. of Governance and Financial Intermediation     Hybrid Journal  
Intl. J. of Granular Computing, Rough Sets and Intelligent Systems     Hybrid Journal   (Followers: 3)
Intl. J. of Green Economics     Hybrid Journal   (Followers: 6, SJR: 0.209, CiteScore: 0)
Intl. J. of Grid and Utility Computing     Hybrid Journal   (SJR: 0.341, CiteScore: 2)
Intl. J. of Happiness and Development     Hybrid Journal   (Followers: 8)
Intl. J. of Healthcare Policy     Hybrid Journal   (Followers: 1)
Intl. J. of Healthcare Technology and Management     Hybrid Journal   (Followers: 7, SJR: 0.139, CiteScore: 0)
Intl. J. of Heavy Vehicle Systems     Hybrid Journal   (Followers: 7, SJR: 0.23, CiteScore: 0)
Intl. J. of High Performance Computing and Networking     Hybrid Journal   (Followers: 4, SJR: 0.428, CiteScore: 1)
Intl. J. of High Performance Systems Architecture     Hybrid Journal   (Followers: 6, SJR: 0.116, CiteScore: 0)
Intl. J. of Higher Education and Sustainability     Hybrid Journal   (Followers: 6)
Intl. J. of Hospitality and Event Management     Hybrid Journal   (Followers: 4)
Intl. J. of Human Factors and Ergonomics     Hybrid Journal   (Followers: 21, SJR: 0.117, CiteScore: 0)
Intl. J. of Human Factors Modelling and Simulation     Hybrid Journal   (Followers: 18)
Intl. J. of Human Resources Development and Management     Hybrid Journal   (Followers: 29, SJR: 0.162, CiteScore: 0)
Intl. J. of Human Rights and Constitutional Studies     Hybrid Journal   (Followers: 14)
Intl. J. of Humanitarian Technology     Hybrid Journal   (Followers: 1)
Intl. J. of Hybrid Intelligence     Hybrid Journal  
Intl. J. of Hydrology Science and Technology     Hybrid Journal   (Followers: 8, SJR: 0.43, CiteScore: 2)
Intl. J. of Hydromechatronics     Hybrid Journal  

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Similar Journals
Journal Cover
International Journal of Computational Biology and Drug Design
Journal Prestige (SJR): 0.231
Citation Impact (citeScore): 1
Number of Followers: 1  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1756-0756 - ISSN (Online) 1756-0764
Published by Inderscience Publishers Homepage  [449 journals]
  • A hidden Markov model-based approach to reconstructing double minute
           chromosome amplicons
    • Authors: Ruslan T. Mardugalliamov, Kamal Al Nasr, Matthew Hayes
      Pages: 5 - 20
      Abstract: Double minute chromosomes (DMs) are circular fragments of extrachromosomal DNA. They cause extreme gene amplification in the cells of malignant tumours. Their existence correlates with malignant tumour cell behaviour and drug resistance. Locating DMs is important for informing precision therapy to cancer treatment. Furthermore, accurate detection of double minutes requires precise reconstruction of their amplicons, which are the highly-amplified gene-carrying contiguous segments that adjoin to form DMs. This work presents AmpliconFinder - a Hidden-Markov Model-based approach to detect DM amplicons. To assess its efficacy, AmpliconFinder was used to augment an earlier framework for DM detection (DMFinder), thus improving its sensitivity and robustness to noisy sequence data. Experiments on simulated genomic data show that augmenting DMFinder with AmpliconFinder significantly increased the sensitivity of DMFinder on these data. Moreover, DMFinder with AmpliconFinder found all previously reported DMs in three pediatric medulloblastoma datasets, whereas the original DMFinder framework found none.
      Keywords: double minute; tumour; next generation sequencing; structural variation; cancer
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 5 - 20
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105096
      Issue No: Vol. 13, No. 1 (2020)
       
  • A De-Novo drug design and ADMET study to design small molecule stabilisers
           targeting mutant (V210I) human prion protein against familial
           Creutzfeldt-Jakob disease (fCJD)
    • Authors: Rafat Alam, G.M. Sayedur Rahman, Nahid Hasan, Abu Sayeed Chowdhury
      Pages: 21 - 35
      Abstract: The purpose of our project was to computationally design small molecule stabilisers targeting mutant (V210I) human prion protein (HuPrP) using combined De-novo pharmacophore based drug design and virtual molecular docking. The newly designed molecules were also analysed so it might qualify as a new cure for the familial Creutzfeldt-Jakob disease (fCJD). We collected the target protein structure from protein data bank (RCSB PDB). and minimised the energy using Yasara energy minimisation webserver and validated the structure using RAMPAGE webserver. We used KV Finder, a plug-in of Pymol to identify the drug binding pockets in the target protein. The pocket information was used for de-novo ligand design using the e-LEA3D webserver. Those ligands were used to generate a pharmacophore using LigandScout for the selected pockets. The pharmacophores were used as the search templates using Pharmit for the virtual screening of small molecules from Pubchem database followed by the docking of the screened small molecules in the pockets using Autodock Vina. Best five molecules were selected for ADMET properties using SwissADME. All the five small molecules were proven to be the ideal candidates for further drug development.
      Keywords: ADMET; absorption; distribution; metabolism; excretion; toxicity; de-novo drug design; docking; prion; PDB; pharmacophore
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 21 - 35
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105103
      Issue No: Vol. 13, No. 1 (2020)
       
  • Drug-drug interaction prediction based on co-medication patterns
           and graph matching
    • Authors: Wen-Hao Chiang, Li Shen, Lang Li, Xia Ning
      Pages: 36 - 57
      Abstract: High-order drug-drug interactions (DDIs) and associated adverse drug reactions (ADRs) are common, particularly for elderly people, and therefore represent a significant public health problem. In this paper, the problem of predicting whether a drug combination of arbitrary orders is likely to induce adverse drug reactions is considered. To solve this problem, novel kernels over drug combinations of arbitrary orders are developed within support vector machines (SVMs) for the prediction. Graph matching methods are used in the novel kernels to measure the similarities among drug combinations, in which drug co-medication patterns are leveraged to measure single drug similarities. The experimental results on a real-world dataset demonstrated that the new kernels achieve an area under the curve (AUC) value 0.912 for the prediction problem. The new methods with drug co-medication based single drug similarities can accurately predict whether a drug combination is likely to induce adverse drug reactions of interest.
      Keywords: drug-drug interaction prediction; drug combination similarity; comedication; graph matching; arbitrary order; adverse drug reaction; myopathy; single drug similarity; SVMs; support vector machines; binary classification problem
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 36 - 57
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105093
      Issue No: Vol. 13, No. 1 (2020)
       
  • Brain-wide structural connectivity alterations under the control of
           Alzheimer risk genes
    • Authors: Jingwen Yan, V. Vinesh Raja, Zhi Huang, Enrico Amico, Kwangsik Nho, Shiaofen Fang, Olaf Sporns, Yu-chien Wu, Andrew Saykin, Joaquín Goñi, Li Shen
      Pages: 58 - 70
      Abstract: Alzheimer's disease is the most common form of brain dementia characterised by gradual loss of memory. Large-scale genome-wide association studies (GWASs) have identified some AD risk genes, but their relationship with the brain-wide network breakdown in AD remains unknown. Using the genotype and diffusion tensor imaging (DTI) data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we performed a targeted genetic association analysis of three types of link measures, including fibre anisotropy, fibre length and density. For fair comparison, all link measures were normalised with zero mean and unit standard deviation. We focused on 34 AD risk SNPs identified in previous GWAS studies. After Bonferroni correction, rs10498633 in SLC24A4 was found to be significantly associated with anisotropy, total number and length of fibres. rs429358 in top AD risk gene APOE showed nominal significance of association with the density of fibres between subcortical and cerebellum regions.
      Keywords: brain connectivity; imaging genetics association; Alzheimer's disease
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 58 - 70
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105098
      Issue No: Vol. 13, No. 1 (2020)
       
  • High scoring segment selection for pairwise whole genome sequence
           alignment with the maximum scoring subsequence and GPUs
    • Authors: Abdulrhman Aljouie, Ling Zhong, Usman Roshan
      Pages: 71 - 81
      Abstract: Whole genome alignment programs use string matching with hash tables to identify high scoring fragments between a query and target sequence around which a full alignment is then built. A recent study comparing alignment programs showed that while evolutionary similar genomes were easy to align, divergent genomes still posed a challenge to existing methods. To fill this gap we explore the use of the maximum scoring subsequence to identify high scoring fragments. We split the query genome into several fragments and align them to the target with a previously published parallel algorithm for short read alignment. We then pass such high scoring fragments on to the LASTZ program to obtain a more complete alignment. On simulated data we obtain an average of at least 20% higher accuracy than the alignment given by LASTZ at the expense of few hours of additional runtime. Our source code is freely available at http://web.njit.edu/usman/MSGA
      Keywords: genome alignment; anchor selection; LASTZ; GPU; graphics processing unit
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 71 - 81
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105097
      Issue No: Vol. 13, No. 1 (2020)
       
  • Pessimistic optimisation for modelling microbial communities with
           uncertainty
    • Authors: Meltem Apaydin, Liang Xu, Bo Zeng, Xiaoning Qian
      Pages: 82 - 97
      Abstract: Optimisation-based mathematical models provide ways to analyse and obtain predictions on microbial communities who play critical roles in the ecological system, human health and diseases. However, there are inherent model and data uncertainties from the existing knowledge and experiments so that the imposed models may not exactly reflect the reality in nature. Here, we aim to have a flexible framework to model microbial communities with uncertainty, and introduce P-OptCom, an extension of an existing method OptCom, based on pessimistic bilevel optimisation. This framework relies on the coordinated decision making between the single upper-level and multiple lower-level decision makers to better approximate community steady states even when the individual microorganisms' behavior deviate from the optimum in terms of their cellular fitness criteria. Our study demonstrates that without experimental knowledge in advance, we are able to analyse the trade-offs among the members of microbial communities and closely approximate the actual experimental measurements.
      Keywords: microbial communities; pessimistic bilevel optimisation; stoichiometric-based genome-scale metabolic modelling
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 82 - 97
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105094
      Issue No: Vol. 13, No. 1 (2020)
       
  • Boosting gene expression clustering with system-wide biological
           information: a robust autoencoder approach
    • Authors: Hongzhu Cui, Chong Zhou, Xinyu Dai, Yuting Liang, Randy Paffenroth, Dmitry Korkin
      Pages: 98 - 123
      Abstract: One of the first computational steps in exploration and analysis of the gene expression data is clustering. However, most of the standard clustering methods do not take prior biological information into account. Here, we propose a new approach for gene expression clustering analysis. The approach benefits from a new deep learning architecture, Robust Autoencode, and from incorporating prior system-wide biological information into the clustering process. We tested our approach on two gene expression datasets. Our approach outperformed all other clustering methods on the labelled yeast gene expression dataset. Furthermore, we showed that it is better in identifying the functionally common clusters on the unlabelled human gene expression dataset. The results demonstrate that our new deep learning architecture can generalise well the specific properties of gene expression profiles. Furthermore, the results confirm our hypothesis that the prior biological network knowledge is helpful in the gene expression clustering.
      Keywords: gene expression; PPIs; protein-protein interactions; clustering; deep learning
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 98 - 123
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105113
      Issue No: Vol. 13, No. 1 (2020)
       
  • Modelling of hypoxia gene expression for three different cancer cell lines
    • Authors: Babak Soltanalizadeh, Erika Gonzalez Rodriguez, Vahed Maroufy, W. Jim Zheng, Hulin Wu
      Pages: 124 - 143
      Abstract: Gene dynamic analysis is essential in identifying target genes involved in the pathogenesis of various diseases, including cancer. Hypoxia often influences cancer prognosis. We applied a multi-step pipeline to study dynamic gene expressions in response to hypoxia in three cancer cell lines: prostate (DU145), colon (HT29), and breast (MCF7). We identified 26 distinct temporal expression patterns in DU145 and 29 patterns in HT29 and MCF7. Module-based dynamic networks were developed for each cell line. Because our analyses exploited the time-dependent nature of gene expression for identifying significant genes novel significant genes and transcription factors were identified. Our gene network returned significant information regarding biologically important modules of genes. In particular, results suggest that changes expression of BMP6 and ARSJ might play a key role in the time-dependent response to hypoxia in breast cancer. Furthermore, the network can potentially learn the regulatory path between transcription factors and the downstream genes.
      Keywords: gene expression; hypoxia; colon cancer; breast cancer; prostate cancer; significant genes; BMP6; ARSJ
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 124 - 143
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105115
      Issue No: Vol. 13, No. 1 (2020)
       
  • TopQA: a topological representation for single-model protein quality
           assessment with machine learning
    • Authors: John Smith, Matthew Conover, Natalie Stephenson, Jesse Eickholt, Dong Si, Miao Sun, Renzhi Cao
      Pages: 144 - 153
      Abstract: Correctly predicting the complex three-dimensional structure of a protein from its sequence would allow for a superior understanding of the function of specific proteins with many applications. We propose a novel method aimed to tackle a crucial step in the protein prediction problem, assessing the quality of generated predictions. Unlike traditional methods, our method, to the best of our knowledge, is the first to analyse the topology of the predicted structure. We found that our new representation provided accurate information regarding the location of the protein's backbone. Using this information, we implemented a novel algorithm based on convolutional neural network (CNN) to predict GDT_TS score for given protein models. Our method has shown promising results - overall correlation of 0.41 on CASP12 dataset. Future work will aim to implement additional features into our representation. The software is freely available at GitHub: https://github.com/caorenzhi/TopQA.
      Keywords: CNN; convolutional neural network; protein single-model quality assessment; topological representation
      Citation: International Journal of Computational Biology and Drug Design, Vol. 13, No. 1 (2020) pp. 144 - 153
      PubDate: 2020-02-13T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2020.105095
      Issue No: Vol. 13, No. 1 (2020)
       
 
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