Use all functions optimally: LOGIN NOW

    Detection of Intramolecular Tunnels Connecting Sequence of Sites in Protein Structures (English)

    In: 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014) ;  Chapter: 9  ; 73-80  ; 2014

    How to get this title?

    Check access
    Download
    Commercial Copyright fee: €29.95 Basic fee: €4.00 Total price: €33.95
    Academic Copyright fee: €15.00 Basic fee: €2.00 Total price: €17.00

    Export, share and cite

    Proteins are essential for functioning of all living organisms and studying their inner structure and functions has been of a high importance. Many studies concentrated on detection of various inner structures inside macromolecules (e.g. tunnels, channels, pores) which play an essential role in the functioning of a large number of proteins. Here we present a novel approach to a detection of intramolecular tunnels. These pathways may facilitate the transport of reaction intermediates among buried active sites. The results obtained by the proposed algorithm were compared to intramolecular tunnels whose presence in given structures is already known. The algorithm is able to also identify other inner structures, such as channels or pores.

    Table of contents eBook

    The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

    1
    Agent-Based Model for Phenotypic Prediction Using Genomic and Environmental Data
    Alameda, Sebastien / Bernon, Carole / Mano, Jean-Pierre et al. | 2014
    2
    NAPROC-13: A Carbon NMR Web Database for the Structural Elucidation of Natural Products and Food Phytochemicals
    López-Pérez, José Luis / Theron, Roberto / del Olmo, Esther / Santos-Buitrago, Beatriz / Adserias, José Francisco / Estévez, Carlos / Cuadrado, Carlos García / López, David Eguiluz / Santos-García, Gustavo et al. | 2014
    3
    Platform Image Processing Applied to the Study of Retinal Vessels
    Chamoso, Pablo / García-Ortiz, Luis / Recio-Rodríguez, José I. / Gómez-Marcos, Manuel A. et al. | 2014
    4
    Improving miRNA Classification Using an Exhaustive Set of Features
    ElGokhy, Sherin M. / Shibuya, Tetsuo / Shoukry, Amin et al. | 2014
    5
    Designing an Ontology Tool for the Unification of Biofilms Data
    Sousa, Ana Margarida / Pereira, Maria Olívia / Azevedo, Nuno F. / Lourenço, Anália et al. | 2014
    6
    BEW: Bioinformatics Workbench for Analysis of Biofilms Experimental Data
    Rodríguez, Gael Pérez / Glez-Peña, Daniel / Azevedo, Nuno F. / Pereira, Maria Olívia / Fdez-Riverola, Florentino / Lourenço, Anália et al. | 2014
    7
    Discrimination of Brazilian Cassava Genotypes (Manihot esculenta Crantz) According to Their Physicochemical Traits and Functional Properties through Bioinformatics Tools
    Moresco, Rodolfo / Uarrota, Virgílio G. / Nunes, Eduardo da C. / Coelho, Bianca / Amante, Edna Regina / Gervin, Vanessa Maria / Campos, Carlos Eduardo M. / Rocha, Miguel / Maraschin, Marcelo et al. | 2014
    8
    Prediction of Active Residues of β-galactosidase from Bacteroides thetaiotaomicron
    Vukić, Vladimir / Hrnjez, Dajana / Milanović, Spasenija / Iličić, Mirela / Kanurić, Katarina / Petri, Edward et al. | 2014
    9
    Detection of Intramolecular Tunnels Connecting Sequence of Sites in Protein Structures
    Strnad, Ondrej / Kozlikova, Barbora / Sochor, Jiri et al. | 2014
    10
    Improving Positive Unlabeled Learning Algorithms for Protein Interaction Prediction
    Pancaroglu, Doruk / Tan, Mehmet et al. | 2014
    11
    Finding Class C GPCR Subtype-Discriminating N-grams through Feature Selection
    König, Caroline / Alquézar, René / Vellido, Alfredo / Giraldo, Jesús et al. | 2014
    12
    Geometric Approach to Biosequence Analysis
    Brimkov, Boris / Brimkov, Valentin E. et al. | 2014
    13
    Timed and Probabilistic Model Checking over Phylogenetic Trees
    Requeno, José Ignacio / Colom, José Manuel et al. | 2014
    14
    mBWA: A Massively Parallel Sequence Reads Aligner
    Cui, Yingbo / Liao, Xiangke / Zhu, Xiaoqian / Wang, Bingqiang / Peng, Shaoliang et al. | 2014
    15
    Optimizing Multiple Pairwise Alignment of Genomic Sequences in Multicore Clusters
    Montañola, Alberto / Roig, Concepció / Hernández, Porfidio et al. | 2014
    16
    High Performance Genomic Sequencing: A Filtered Approach
    Retamosa, German / de Pedro, Luis / Gonzalez, Ivan / Tamames, Javier et al. | 2014
    17
    Exceptional Single Strand DNA Word Symmetry: Universal Law?
    Afreixo, Vera / Rodrigues, João M. O. S. / Bastos, Carlos A. C. et al. | 2014
    18
    Mutation Analysis in PARK2 Gene Uncovers Patterns of Associated Genetic Variants
    Castro, Luísa / Oliveira, José Luís / Silva, Raquel M. et al. | 2014
    19
    Heterogeneous Parallelization of Aho-Corasick Algorithm
    Soroushnia, Shima / Daneshtalab, Masoud / Plosila, Juha / Liljeberg, Pasi et al. | 2014
    20
    High-Confidence Predictions in Systems Biology Dynamic Models
    Villaverde, Alejandro F. / Bongard, Sophia / Mauch, Klaus / Müller, Dirk / Balsa-Canto, Eva / Schmid, Joachim / Banga, Julio R. et al. | 2014
    21
    A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems
    Penas, D. R. / Banga, Julio R. / González, P. / Doallo, R. et al. | 2014
    22
    A Method to Calibrate Metabolic Network Models with Experimental Datasets
    Perez-Garcia, Octavio / Villas-Boas, Silas / Singhal, Naresh et al. | 2014
    23
    Metagenomic Analysis of the Saliva Microbiome with Merlin
    Barbosa, Pedro / Dias, Oscar / Arrais, Joel P. / Rocha, Miguel et al. | 2014
    24
    Networking the Way towards Antimicrobial Combination Therapies
    Jorge, Paula / Pereira, Maria Olívia / Lourenc̨o, Anália et al. | 2014
    25
    A Logic Computational Framework to Query Dynamics on Complex Biological Pathways
    Santos-García, Gustavo / De Las Rivas, Javier / Talcott, Carolyn et al. | 2014
    26
    Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies
    Liu, F. / Vilaça, P. / Rocha, I. / Rocha, M. et al. | 2014
    27
    T-HMM: A Novel Biomedical Text Classifier Based on Hidden Markov Models
    Vieira, A. Seara / Iglesias, E. L. / Borrajo, L. et al. | 2014
    28
    TIDA: A Spanish EHR Semantic Search Engine
    Costumero, Roberto / Gonzalo, Consuelo / Menasalvas, Ernestina et al. | 2014
    29
    BioClass: A Tool for Biomedical Text Classification
    Romero, R. / Vieira, A. Seara / Iglesias, E. L. / Borrajo, L. et al. | 2014
    30
    Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features
    Lamurias, Andre / Ferreira, João / Couto, Francisco M. et al. | 2014
    31
    Bringing Named Entity Recognition on Drupal Content Management System
    Ferrnandes, José / Lourenço, Anália et al. | 2014
    32
    Marky: A Lightweight Web Tracking Tool for Document Annotation
    Pérez-Pérez, Martín / Glez-Peña, Daniel / Fdez-Riverola, Florentino / Lourenço, Anália et al. | 2014
    33
    A Nanopublishing Architecture for Biomedical Data
    Sernadela, Pedro / van der Horst, Eelke / Thompson, Mark / Lopes, Pedro / Roos, Marco / Oliveira, José Luís et al. | 2014
    34
    Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis
    Krallinger, Martin / Leitner, Florian / Valencia, Alfonso et al. | 2014

    How to get this title?

    Check access
    Download
    Commercial Copyright fee: €29.95 Basic fee: €4.00 Total price: €33.95
    Academic Copyright fee: €15.00 Basic fee: €2.00 Total price: €17.00

    Export, share and cite

    Feedback