for Journals by Title or ISSN
for Articles by Keywords
help

Publisher: Hindawi   (Total: 338 journals)

 A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z  

        1 2 | Last   [Sort by number of followers]   [Restore default list]

Showing 1 - 200 of 338 Journals sorted alphabetically
Abstract and Applied Analysis     Open Access   (Followers: 3, SJR: 0.343, CiteScore: 1)
Active and Passive Electronic Components     Open Access   (Followers: 7, SJR: 0.136, CiteScore: 0)
Advances in Acoustics and Vibration     Open Access   (Followers: 36, SJR: 0.147, CiteScore: 0)
Advances in Aerospace Engineering     Open Access   (Followers: 53)
Advances in Agriculture     Open Access   (Followers: 9)
Advances in Artificial Intelligence     Open Access   (Followers: 15)
Advances in Astronomy     Open Access   (Followers: 39, SJR: 0.257, CiteScore: 1)
Advances in Bioinformatics     Open Access   (Followers: 17, SJR: 0.565, CiteScore: 2)
Advances in Biology     Open Access   (Followers: 9)
Advances in Chemistry     Open Access   (Followers: 22)
Advances in Civil Engineering     Open Access   (Followers: 41, SJR: 0.539, CiteScore: 1)
Advances in Computer Engineering     Open Access   (Followers: 4)
Advances in Condensed Matter Physics     Open Access   (Followers: 10, SJR: 0.315, CiteScore: 1)
Advances in Decision Sciences     Open Access   (Followers: 3, SJR: 0.303, CiteScore: 1)
Advances in Electrical Engineering     Open Access   (Followers: 31)
Advances in Electronics     Open Access   (Followers: 70)
Advances in Emergency Medicine     Open Access   (Followers: 12)
Advances in Endocrinology     Open Access   (Followers: 5)
Advances in Environmental Chemistry     Open Access   (Followers: 7)
Advances in Epidemiology     Open Access   (Followers: 8)
Advances in Fuzzy Systems     Open Access   (Followers: 5, SJR: 0.161, CiteScore: 1)
Advances in Geology     Open Access   (Followers: 19)
Advances in Geriatrics     Open Access   (Followers: 5)
Advances in Hematology     Open Access   (Followers: 11, SJR: 0.661, CiteScore: 2)
Advances in Hepatology     Open Access   (Followers: 2)
Advances in High Energy Physics     Open Access   (Followers: 19, SJR: 0.866, CiteScore: 2)
Advances in Human-Computer Interaction     Open Access   (Followers: 20, SJR: 0.186, CiteScore: 1)
Advances in Materials Science and Engineering     Open Access   (Followers: 30, SJR: 0.315, CiteScore: 1)
Advances in Mathematical Physics     Open Access   (Followers: 4, SJR: 0.218, CiteScore: 1)
Advances in Medicine     Open Access   (Followers: 3)
Advances in Meteorology     Open Access   (Followers: 21, SJR: 0.48, CiteScore: 1)
Advances in Multimedia     Open Access   (Followers: 1, SJR: 0.173, CiteScore: 1)
Advances in Nonlinear Optics     Open Access   (Followers: 6)
Advances in Numerical Analysis     Open Access   (Followers: 5)
Advances in Nursing     Open Access   (Followers: 29)
Advances in Operations Research     Open Access   (Followers: 12, SJR: 0.205, CiteScore: 1)
Advances in Optical Technologies     Open Access   (Followers: 4, SJR: 0.214, CiteScore: 1)
Advances in Optics     Open Access   (Followers: 5)
Advances in OptoElectronics     Open Access   (Followers: 6, SJR: 0.141, CiteScore: 0)
Advances in Orthopedics     Open Access   (Followers: 8, SJR: 0.922, CiteScore: 2)
Advances in Pharmacological Sciences     Open Access   (Followers: 8, SJR: 0.591, CiteScore: 2)
Advances in Physical Chemistry     Open Access   (Followers: 10, SJR: 0.179, CiteScore: 1)
Advances in Power Electronics     Open Access   (Followers: 33, SJR: 0.184, CiteScore: 0)
Advances in Preventive Medicine     Open Access   (Followers: 6)
Advances in Public Health     Open Access   (Followers: 23)
Advances in Regenerative Medicine     Open Access   (Followers: 2)
Advances in Software Engineering     Open Access   (Followers: 10)
Advances in Statistics     Open Access   (Followers: 4)
Advances in Toxicology     Open Access   (Followers: 2)
Advances in Tribology     Open Access   (Followers: 13, SJR: 0.265, CiteScore: 1)
Advances in Urology     Open Access   (Followers: 9, SJR: 0.51, CiteScore: 1)
Advances in Virology     Open Access   (Followers: 7, SJR: 0.838, CiteScore: 2)
AIDS Research and Treatment     Open Access   (Followers: 3, SJR: 0.758, CiteScore: 2)
Analytical Cellular Pathology     Open Access   (Followers: 2, SJR: 0.886, CiteScore: 2)
Anatomy Research Intl.     Open Access   (Followers: 2)
Anemia     Open Access   (Followers: 5, SJR: 0.669, CiteScore: 2)
Anesthesiology Research and Practice     Open Access   (Followers: 14, SJR: 0.501, CiteScore: 1)
Applied and Environmental Soil Science     Open Access   (Followers: 17, SJR: 0.451, CiteScore: 1)
Applied Bionics and Biomechanics     Open Access   (Followers: 8, SJR: 0.288, CiteScore: 1)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 13)
Archaea     Open Access   (Followers: 3, SJR: 0.852, CiteScore: 2)
Arthritis     Open Access   (Followers: 5, SJR: 0.454, CiteScore: 1)
Autism Research and Treatment     Open Access   (Followers: 26)
Autoimmune Diseases     Open Access   (Followers: 4, SJR: 0.805, CiteScore: 2)
Behavioural Neurology     Open Access   (Followers: 9, SJR: 0.786, CiteScore: 2)
Biochemistry Research Intl.     Open Access   (Followers: 6, SJR: 0.437, CiteScore: 2)
Bioinorganic Chemistry and Applications     Open Access   (Followers: 10, SJR: 0.419, CiteScore: 2)
BioMed Research Intl.     Open Access   (Followers: 4, SJR: 0.935, CiteScore: 3)
Biotechnology Research Intl.     Open Access   (Followers: 1)
Bone Marrow Research     Open Access   (Followers: 2, SJR: 0.531, CiteScore: 1)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 4, SJR: 0.867, CiteScore: 1)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 5, SJR: 0.548, CiteScore: 1)
Canadian Respiratory J.     Open Access   (Followers: 1, SJR: 0.474, CiteScore: 1)
Cardiology Research and Practice     Open Access   (Followers: 8, SJR: 1.237, CiteScore: 4)
Case Reports in Anesthesiology     Open Access   (Followers: 10)
Case Reports in Cardiology     Open Access   (Followers: 3, SJR: 0.219, CiteScore: 0)
Case Reports in Critical Care     Open Access   (Followers: 8)
Case Reports in Dentistry     Open Access   (Followers: 5, SJR: 0.229, CiteScore: 0)
Case Reports in Dermatological Medicine     Open Access   (Followers: 2)
Case Reports in Emergency Medicine     Open Access   (Followers: 14)
Case Reports in Endocrinology     Open Access   (Followers: 1, SJR: 0.209, CiteScore: 1)
Case Reports in Gastrointestinal Medicine     Open Access   (Followers: 2)
Case Reports in Genetics     Open Access   (Followers: 1)
Case Reports in Hematology     Open Access   (Followers: 4)
Case Reports in Hepatology     Open Access   (Followers: 1)
Case Reports in Immunology     Open Access   (Followers: 4)
Case Reports in Infectious Diseases     Open Access   (Followers: 5)
Case Reports in Medicine     Open Access   (Followers: 2)
Case Reports in Nephrology     Open Access   (Followers: 4)
Case Reports in Neurological Medicine     Open Access   (Followers: 1)
Case Reports in Obstetrics and Gynecology     Open Access   (Followers: 10)
Case Reports in Oncological Medicine     Open Access   (Followers: 2, SJR: 0.204, CiteScore: 1)
Case Reports in Ophthalmological Medicine     Open Access   (Followers: 3)
Case Reports in Orthopedics     Open Access   (Followers: 5)
Case Reports in Otolaryngology     Open Access   (Followers: 6)
Case Reports in Pathology     Open Access   (Followers: 5)
Case Reports in Pediatrics     Open Access   (Followers: 6)
Case Reports in Psychiatry     Open Access   (Followers: 13)
Case Reports in Pulmonology     Open Access   (Followers: 3)
Case Reports in Radiology     Open Access   (Followers: 9)
Case Reports in Rheumatology     Open Access   (Followers: 6)
Case Reports in Surgery     Open Access   (Followers: 11)
Case Reports in Transplantation     Open Access  
Case Reports in Urology     Open Access   (Followers: 9)
Case Reports in Vascular Medicine     Open Access  
Case Reports in Veterinary Medicine     Open Access   (Followers: 6)
Child Development Research     Open Access   (Followers: 18, SJR: 0.144, CiteScore: 0)
Chinese J. of Engineering     Open Access   (Followers: 2, SJR: 0.114, CiteScore: 0)
Chinese J. of Mathematics     Open Access  
Cholesterol     Open Access   (Followers: 1, SJR: 0.424, CiteScore: 1)
Chromatography Research Intl.     Open Access   (Followers: 6)
Complexity     Hybrid Journal   (Followers: 6, SJR: 0.531, CiteScore: 2)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2, SJR: 0.403, CiteScore: 1)
Computational Intelligence and Neuroscience     Open Access   (Followers: 11, SJR: 0.326, CiteScore: 1)
Contrast Media & Molecular Imaging     Open Access   (Followers: 3, SJR: 0.842, CiteScore: 3)
Critical Care Research and Practice     Open Access   (Followers: 10, SJR: 0.499, CiteScore: 1)
Current Gerontology and Geriatrics Research     Open Access   (Followers: 9, SJR: 0.512, CiteScore: 2)
Depression Research and Treatment     Open Access   (Followers: 14, SJR: 0.816, CiteScore: 2)
Dermatology Research and Practice     Open Access   (Followers: 3, SJR: 0.806, CiteScore: 2)
Diagnostic and Therapeutic Endoscopy     Open Access   (SJR: 0.201, CiteScore: 1)
Discrete Dynamics in Nature and Society     Open Access   (Followers: 5, SJR: 0.279, CiteScore: 1)
Disease Markers     Open Access   (Followers: 1, SJR: 0.9, CiteScore: 2)
Economics Research Intl.     Open Access   (Followers: 1)
Education Research Intl.     Open Access   (Followers: 19)
Emergency Medicine Intl.     Open Access   (Followers: 9, SJR: 0.298, CiteScore: 1)
Enzyme Research     Open Access   (Followers: 4, SJR: 0.653, CiteScore: 3)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 19, SJR: 0.683, CiteScore: 2)
Game Theory     Open Access   (Followers: 1)
Gastroenterology Research and Practice     Open Access   (Followers: 2, SJR: 0.768, CiteScore: 2)
Genetics Research Intl.     Open Access   (Followers: 1, SJR: 0.61, CiteScore: 2)
Geofluids     Open Access   (Followers: 4, SJR: 0.952, CiteScore: 2)
Hepatitis Research and Treatment     Open Access   (Followers: 6, SJR: 0.389, CiteScore: 2)
HPB Surgery     Open Access   (Followers: 6, SJR: 0.824, CiteScore: 2)
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 5, SJR: 1.27, CiteScore: 2)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 1, SJR: 0.627, CiteScore: 2)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 74, SJR: 0.232, CiteScore: 1)
Intl. J. of Agronomy     Open Access   (Followers: 6, SJR: 0.311, CiteScore: 1)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 11, SJR: 0.787, CiteScore: 3)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 21, SJR: 0.285, CiteScore: 1)
Intl. J. of Antennas and Propagation     Open Access   (Followers: 11, SJR: 0.233, CiteScore: 1)
Intl. J. of Atmospheric Sciences     Open Access   (Followers: 21)
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 4, SJR: 0.511, CiteScore: 2)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 3, SJR: 0.501, CiteScore: 2)
Intl. J. of Breast Cancer     Open Access   (Followers: 13, SJR: 1.025, CiteScore: 2)
Intl. J. of Cell Biology     Open Access   (Followers: 3, SJR: 1.887, CiteScore: 4)
Intl. J. of Chemical Engineering     Open Access   (Followers: 8, SJR: 0.327, CiteScore: 1)
Intl. J. of Chronic Diseases     Open Access   (Followers: 1)
Intl. J. of Combinatorics     Open Access   (Followers: 1)
Intl. J. of Computer Games Technology     Open Access   (Followers: 10, SJR: 0.287, CiteScore: 2)
Intl. J. of Corrosion     Open Access   (Followers: 10, SJR: 0.194, CiteScore: 1)
Intl. J. of Dentistry     Open Access   (Followers: 6, SJR: 0.649, CiteScore: 2)
Intl. J. of Differential Equations     Open Access   (Followers: 7, SJR: 0.191, CiteScore: 0)
Intl. J. of Digital Multimedia Broadcasting     Open Access   (Followers: 5, SJR: 0.296, CiteScore: 2)
Intl. J. of Electrochemistry     Open Access   (Followers: 8)
Intl. J. of Endocrinology     Open Access   (Followers: 4, SJR: 1.012, CiteScore: 3)
Intl. J. of Engineering Mathematics     Open Access   (Followers: 5)
Intl. J. of Food Science     Open Access   (Followers: 4, SJR: 0.44, CiteScore: 2)
Intl. J. of Forestry Research     Open Access   (Followers: 3, SJR: 0.373, CiteScore: 1)
Intl. J. of Genomics     Open Access   (Followers: 2, SJR: 0.868, CiteScore: 3)
Intl. J. of Geophysics     Open Access   (Followers: 4, SJR: 0.182, CiteScore: 1)
Intl. J. of Hepatology     Open Access   (Followers: 4, SJR: 0.874, CiteScore: 2)
Intl. J. of Hypertension     Open Access   (Followers: 6, SJR: 0.578, CiteScore: 1)
Intl. J. of Inflammation     Open Access   (SJR: 1.264, CiteScore: 3)
Intl. J. of Inorganic Chemistry     Open Access   (Followers: 3)
Intl. J. of Manufacturing Engineering     Open Access   (Followers: 2)
Intl. J. of Mathematics and Mathematical Sciences     Open Access   (Followers: 3, SJR: 0.177, CiteScore: 0)
Intl. J. of Medicinal Chemistry     Open Access   (Followers: 6, SJR: 0.31, CiteScore: 1)
Intl. J. of Metals     Open Access   (Followers: 4)
Intl. J. of Microbiology     Open Access   (Followers: 4, SJR: 0.662, CiteScore: 2)
Intl. J. of Microwave Science and Technology     Open Access   (Followers: 3, SJR: 0.136, CiteScore: 1)
Intl. J. of Navigation and Observation     Open Access   (Followers: 20, SJR: 0.267, CiteScore: 2)
Intl. J. of Nephrology     Open Access   (Followers: 1, SJR: 0.697, CiteScore: 1)
Intl. J. of Oceanography     Open Access   (Followers: 7)
Intl. J. of Optics     Open Access   (Followers: 7, SJR: 0.231, CiteScore: 1)
Intl. J. of Otolaryngology     Open Access   (Followers: 3)
Intl. J. of Partial Differential Equations     Open Access   (Followers: 2)
Intl. J. of Pediatrics     Open Access   (Followers: 6)
Intl. J. of Peptides     Open Access   (Followers: 4, SJR: 0.46, CiteScore: 1)
Intl. J. of Photoenergy     Open Access   (Followers: 2, SJR: 0.341, CiteScore: 1)
Intl. J. of Plant Genomics     Open Access   (Followers: 4, SJR: 0.583, CiteScore: 1)
Intl. J. of Polymer Science     Open Access   (Followers: 24, SJR: 0.298, CiteScore: 1)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Quality, Statistics, and Reliability     Open Access   (Followers: 15)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.123, CiteScore: 1)
Intl. J. of Reproductive Medicine     Open Access   (Followers: 4)
Intl. J. of Rheumatology     Open Access   (Followers: 4, SJR: 0.645, CiteScore: 2)
Intl. J. of Rotating Machinery     Open Access   (Followers: 2, SJR: 0.193, CiteScore: 1)
Intl. J. of Spectroscopy     Open Access   (Followers: 7)
Intl. J. of Stochastic Analysis     Open Access   (Followers: 3, SJR: 0.279, CiteScore: 1)
Intl. J. of Surgical Oncology     Open Access   (Followers: 1, SJR: 0.573, CiteScore: 2)
Intl. J. of Telemedicine and Applications     Open Access   (Followers: 5, SJR: 0.403, CiteScore: 2)
Intl. J. of Vascular Medicine     Open Access   (SJR: 0.782, CiteScore: 2)
Intl. J. of Zoology     Open Access   (Followers: 2, SJR: 0.209, CiteScore: 1)
Intl. Scholarly Research Notices     Open Access   (Followers: 191)
ISRN Astronomy and Astrophysics     Open Access   (Followers: 7)
J. of Addiction     Open Access   (Followers: 12)
J. of Advanced Transportation     Hybrid Journal   (Followers: 13, SJR: 0.581, CiteScore: 1)
J. of Aerodynamics     Open Access   (Followers: 12)

        1 2 | Last   [Sort by number of followers]   [Restore default list]

Journal Cover
Advances in Bioinformatics
Journal Prestige (SJR): 0.565
Citation Impact (citeScore): 2
Number of Followers: 17  

  This is an Open Access Journal Open Access journal
ISSN (Print) 1687-8027 - ISSN (Online) 1687-8035
Published by Hindawi Homepage  [338 journals]
  • In Silico Characterization and Structural Modeling of Dermacentor
           andersoni p36 Immunosuppressive Protein

    • Abstract: Ticks cause approximately $17–19 billion economic losses to the livestock industry globally. Development of recombinant antitick vaccine is greatly hindered by insufficient knowledge and understanding of proteins expressed by ticks. Ticks secrete immunosuppressant proteins that modulate the host’s immune system during blood feeding; these molecules could be a target for antivector vaccine development. Recombinant p36, a 36 kDa immunosuppressor from the saliva of female Dermacentor andersoni, suppresses T-lymphocytes proliferation in vitro. To identify potential unique structural and dynamic properties responsible for the immunosuppressive function of p36 proteins, this study utilized bioinformatic tool to characterize and model structure of D. andersoni p36 protein. Evaluation of p36 protein family as suitable vaccine antigens predicted a p36 homolog in Rhipicephalus appendiculatus, the tick vector of East Coast fever, with an antigenicity score of 0.7701 that compares well with that of Bm86 (0.7681), the protein antigen that constitute commercial tick vaccine Tickgard™. Ab initio modeling of the D. andersoni p36 protein yielded a 3D structure that predicted conserved antigenic region, which has potential of binding immunomodulating ligands including glycerol and lactose, found located within exposed loop, suggesting a likely role in immunosuppressive function of tick p36 proteins. Laboratory confirmation of these preliminary results is necessary in future studies.
      PubDate: Sun, 08 Apr 2018 00:00:00 +000
       
  • Framework for Parallel Preprocessing of Microarray Data Using Hadoop

    • Abstract: Nowadays, microarray technology has become one of the popular ways to study gene expression and diagnosis of disease. National Center for Biology Information (NCBI) hosts public databases containing large volumes of biological data required to be preprocessed, since they carry high levels of noise and bias. Robust Multiarray Average (RMA) is one of the standard and popular methods that is utilized to preprocess the data and remove the noises. Most of the preprocessing algorithms are time-consuming and not able to handle a large number of datasets with thousands of experiments. Parallel processing can be used to address the above-mentioned issues. Hadoop is a well-known and ideal distributed file system framework that provides a parallel environment to run the experiment. In this research, for the first time, the capability of Hadoop and statistical power of R have been leveraged to parallelize the available preprocessing algorithm called RMA to efficiently process microarray data. The experiment has been run on cluster containing 5 nodes, while each node has 16 cores and 16 GB memory. It compares efficiency and the performance of parallelized RMA using Hadoop with parallelized RMA using affyPara package as well as sequential RMA. The result shows the speed-up rate of the proposed approach outperforms the sequential approach and affyPara approach.
      PubDate: Thu, 29 Mar 2018 00:00:00 +000
       
  • Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl
           Peptidase-IV Inhibitor

    • Abstract: The inhibition of dipeptidyl peptidase-IV (DPPIV) is a popular route for the treatment of type-2 diabetes. Commercially available gliptin-based drugs such as sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin were specifically developed as DPPIV inhibitors for diabetic patients. The use of Gynura bicolor in treating diabetes had been reported in various in vitro experiments. However, an understanding of the inhibitory actions of G. bicolor bioactive compounds on DPPIV is still lacking and this may provide crucial information for the development of more potent and natural sources of DPPIV inhibitors. Evaluation of G. bicolor bioactive compounds for potent DPPIV inhibitors was computationally conducted using Lead IT and iGEMDOCK software, and the best free-binding energy scores for G. bicolor bioactive compounds were evaluated in comparison with the commercial DPPIV inhibitors, sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin. Drug-likeness and absorption, distribution, metabolism, and excretion (ADME) analysis were also performed. Based on molecular docking analysis, four of the identified bioactive compounds in G. bicolor, 3-caffeoylquinic acid, 5-O-caffeoylquinic acid, 3,4-dicaffeoylquinic acid, and trans-5-p-coumaroylquinic acid, resulted in lower free-binding energy scores when compared with two of the commercially available gliptin inhibitors. The results revealed that bioactive compounds in G. bicolor are potential natural inhibitors of DPPIV.
      PubDate: Tue, 08 Aug 2017 09:33:15 +000
       
  • Empirical Comparison of Visualization Tools for Larger-Scale Network
           Analysis

    • Abstract: Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. We comment on their strengths and their weaknesses and empirically discuss their scalability, user friendliness, and postvisualization capabilities.
      PubDate: Tue, 18 Jul 2017 00:00:00 +000
       
  • An Efficient Approach in Analysis of DNA Base Calling Using Neural Fuzzy
           Model

    • Abstract: This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base. This is achieving effective results with high performance in employment.
      PubDate: Tue, 31 Jan 2017 05:55:29 +000
       
  • Multiple Linear Regression for Reconstruction of Gene Regulatory Networks
           in Solving Cascade Error Problems

    • Abstract: Gene regulatory network (GRN) reconstruction is the process of identifying regulatory gene interactions from experimental data through computational analysis. One of the main reasons for the reduced performance of previous GRN methods had been inaccurate prediction of cascade motifs. Cascade error is defined as the wrong prediction of cascade motifs, where an indirect interaction is misinterpreted as a direct interaction. Despite the active research on various GRN prediction methods, the discussion on specific methods to solve problems related to cascade errors is still lacking. In fact, the experiments conducted by the past studies were not specifically geared towards proving the ability of GRN prediction methods in avoiding the occurrences of cascade errors. Hence, this research aims to propose Multiple Linear Regression (MLR) to infer GRN from gene expression data and to avoid wrongly inferring of an indirect interaction (A → B → C) as a direct interaction (A → C). Since the number of observations of the real experiment datasets was far less than the number of predictors, some predictors were eliminated by extracting the random subnetworks from global interaction networks via an established extraction method. In addition, the experiment was extended to assess the effectiveness of MLR in dealing with cascade error by using a novel experimental procedure that had been proposed in this work. The experiment revealed that the number of cascade errors had been very minimal. Apart from that, the Belsley collinearity test proved that multicollinearity did affect the datasets used in this experiment greatly. All the tested subnetworks obtained satisfactory results, with AUROC values above 0.5.
      PubDate: Sun, 29 Jan 2017 11:42:15 +000
       
  • Combined Docking with Classical Force Field and Quantum Chemical
           Semiempirical Method PM7

    • Abstract: Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
      PubDate: Mon, 16 Jan 2017 00:00:00 +000
       
 
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
 
Home (Search)
Subjects A-Z
Publishers A-Z
Customise
APIs
Your IP address: 54.161.100.24
 
About JournalTOCs
API
Help
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-