TI2BioP: Topological Indices to BioPolymers. Its practical use to unravel cryptic bacteriocin-like domains
暂无分享,去创建一个
Yunierkis Pérez-Castillo | Reinaldo Molina-Ruiz | Agostinho Antunes | Gisselle Pérez-Machado | Aliuska Morales-Helguera | A. Antunes | Guillermín Agüero-Chapín | Y. Pérez-Castillo | V. Vasconcelos | Guillermín Agüero-Chapin | Vítor Vasconcelos | Reinaldo Molina-Ruiz | Aliuska Morales-Helguera | Gisselle Pérez-Machado | Yunierkis Pérez-Castillo
[1] Mario Soberón,et al. Cryptic endotoxic nature of Bacillus thuringiensis Cry1Ab insecticidal crystal protein , 2004, FEBS letters.
[2] T. Stein. Bacillus subtilis antibiotics: structures, syntheses and specific functions , 2005, Molecular microbiology.
[3] Milan Randic,et al. On the Similarity of DNA Primary Sequences , 2000, J. Chem. Inf. Comput. Sci..
[4] G. A. de la Riva,et al. Role of Tryptophan Residues in Toxicity of Cry1Ab Toxin from Bacillus thuringiensis , 2006, Applied and Environmental Microbiology.
[5] M. Riley,et al. Genetically engineered bacteriocins and their potential as the next generation of antimicrobials. , 2005, Current pharmaceutical design.
[6] Riadh Hammami,et al. BACTIBASE: a new web-accessible database for bacteriocin characterization , 2007, BMC Microbiology.
[7] M. Soberón,et al. Structural and functional analysis of the pre-pore and membrane-inserted pore of Cry1Ab toxin. , 2006, Journal of invertebrate pathology.
[8] M. Lecadet,et al. Distribution of Clostridial cry-Like Genes Among Bacillus thuringiensis and Clostridium Strains , 1998, Current Microbiology.
[9] M. Hasegawa,et al. Novel cry gene from Paenibacillus lentimorbus strain Semadara inhibits ingestion and promotes insecticidal activity in Anomala cuprea larvae. , 2004, Journal of invertebrate pathology.
[10] Lourdes Santana,et al. A QSAR model for in silico screening of MAO-A inhibitors. Prediction, synthesis, and biological assay of novel coumarins. , 2006, Journal of medicinal chemistry.
[11] Yovani Marrero-Ponce,et al. A linear discrimination analysis based virtual screening of trichomonacidal lead-like compounds: outcomes of in silico studies supported by experimental results. , 2005, Bioorganic & medicinal chemistry letters.
[12] S. Gill,et al. Oligomerization triggers binding of a Bacillus thuringiensis Cry1Ab pore-forming toxin to aminopeptidase N receptor leading to insertion into membrane microdomains. , 2004, Biochimica et biophysica acta.
[13] David H Mathews,et al. RNA Secondary Structure Analysis Using RNAstructure , 2006, Current protocols in bioinformatics.
[14] R. P. Ross,et al. Food microbiology: Bacteriocins: developing innate immunity for food , 2005, Nature Reviews Microbiology.
[15] Tight-binding "dihedral orbitals" approach to the degree of folding of macromolecular chains. , 2007, The journal of physical chemistry. B.
[16] K. Wanner,et al. Methods and Principles in Medicinal Chemistry , 2007 .
[17] F. Blecha,et al. Antimicrobial peptides and bacteriocins: alternatives to traditional antibiotics , 2008, Animal Health Research Reviews.
[18] Ernesto Estrada,et al. Spectral Moments of the Edge-Adjacency Matrix of Molecular Graphs, 2. Molecules Containing Heteroatoms and QSAR Applications , 1997, J. Chem. Inf. Comput. Sci..
[19] V. Eijsink,et al. Mutational analysis of the role of tryptophan residues in an antimicrobial peptide. , 2002, Biochemistry.
[20] A Nandy. Recent investigations into global characteristics of long DNA sequences. , 1994, Indian journal of biochemistry & biophysics.
[21] Humberto González Díaz,et al. Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments , 2007, J. Comput. Chem..
[22] Oscar P. Kuipers,et al. BAGEL: a web-based bacteriocin genome mining tool , 2006, Nucleic Acids Res..
[23] Maykel Pérez González,et al. A topological function based on spectral moments for predicting affinity toward A3 adenosine receptors. , 2006, Bioorganic & medicinal chemistry letters.
[24] Robert D. Finn,et al. InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..
[25] A. Bravo. Phylogenetic relationships of Bacillus thuringiensis delta-endotoxin family proteins and their functional domains , 1997, Journal of bacteriology.
[26] Humberto González-Díaz,et al. Biopolymer stochastic moments. I. Modeling human rhinovirus cellular recognition with protein surface electrostatic moments , 2005, Biopolymers.
[27] Svetlana Markovic,et al. Spectral Moments of Phenylenes , 2001, J. Chem. Inf. Comput. Sci..
[28] Ernesto Estrada,et al. Spectral Moments of the Edge Adjacency Matrix in Molecular Graphs, 1. Definition and Applications to the Prediction of Physical Properties of Alkanes , 1996, J. Chem. Inf. Comput. Sci..
[29] O. Sand,et al. The Bacterial Peptide Pheromone Plantaricin A Permeabilizes Cancerous, but not Normal, Rat Pituitary Cells and Differentiates between the Outer and Inner Membrane Leaflet , 2007, Journal of Membrane Biology.
[30] Lourdes Santana,et al. Medicinal chemistry and bioinformatics--current trends in drugs discovery with networks topological indices. , 2007, Current topics in medicinal chemistry.
[31] K. Marchal,et al. Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters , 2004, Peptides.
[32] S. Gill,et al. Mode of action of Bacillus thuringiensis Cry and Cyt toxins and their potential for insect control. , 2007, Toxicon : official journal of the International Society on Toxinology.
[33] Humberto González Díaz,et al. Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices , 2007, J. Comput. Chem..
[34] Humberto González Díaz,et al. Comparative Study of Topological Indices of Macro/Supramolecular RNA Complex Networks , 2008, J. Chem. Inf. Model..
[35] Rolf Apweiler,et al. InterProScan: protein domains identifier , 2005, Nucleic Acids Res..
[36] J. Vederas,et al. Dynamic relationships among type IIa bacteriocins: temperature effects on antimicrobial activity and on structure of the C-terminal amphipathic alpha helix as a receptor-binding region. , 2004, Biochemistry.
[37] Lourdes Santana,et al. Proteomics, networks and connectivity indices , 2008, Proteomics.
[38] Francisco Torrens,et al. Atom, atom-type and total molecular linear indices as a promising approach for bioorganic and medicinal chemistry: theoretical and experimental assessment of a novel method for virtual screening and rational design of new lead anthelmintic. , 2005, Bioorganic & medicinal chemistry.
[39] Humberto González Díaz,et al. QSAR model for alignment‐free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP‐lattice networks , 2008, J. Comput. Chem..
[40] J A Swets,et al. Measuring the accuracy of diagnostic systems. , 1988, Science.
[41] M. Quail,et al. Complete Sequence and Organization of pBtoxis, the Toxin-Coding Plasmid of Bacillus thuringiensis subsp. israelensis , 2002, Applied and Environmental Microbiology.
[42] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[43] A. Nandy. Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences , 1996, Comput. Appl. Biosci..
[44] Humberto González Díaz,et al. MMM-QSAR Recognition of Ribonucleases without Alignment: Comparison with an HMM Model and Isolation from Schizosaccharomyces pombe, Prediction, and Experimental Assay of a New Sequence , 2008, J. Chem. Inf. Model..
[45] Jaap Heringa,et al. SEQATOMS: a web tool for identifying missing regions in PDB in sequence context , 2008, Nucleic Acids Res..
[46] A Atkinson,et al. Using fragment chemistry data mining and probabilistic neural networks in screening chemicals for acute toxicity to the fathead minnow , 2004, SAR and QSAR in environmental research.
[47] J. Tagg,et al. What's in a name? Class distinction for bacteriocins , 2006, Nature Reviews Microbiology.
[48] J. Dorado,et al. Complex network spectral moments for ATCUN motif DNA cleavage: first predictive study on proteins of human pathogen parasites. , 2009, Journal of proteome research.
[49] L. Cruz-Chamorro,et al. In vitro biological activities of magainin alone or in combination with nisin , 2006, Peptides.
[50] Francisco Torrens,et al. 3D-chiral quadratic indices of the 'molecular pseudograph's atom adjacency matrix' and their application to central chirality codification: classification of ACE inhibitors and prediction of sigma-receptor antagonist activities. , 2004, Bioorganic & medicinal chemistry.
[51] Ian Sillitoe,et al. The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies , 2008, Nucleic Acids Res..
[52] Humberto González-Díaz,et al. Predicting stability of Arc repressor mutants with protein stochastic moments. , 2005, Bioorganic & medicinal chemistry.
[53] Ernesto Estrada,et al. In Silico Studies toward the Discovery of New Anti-HIV Nucleoside Compounds with the Use of TOPS-MODE and 2D/3D Connectivity Indices, 1. Pyrimidyl Derivatives , 2002, J. Chem. Inf. Comput. Sci..
[54] Ernesto Estrada,et al. Tight-binding ‘dihedral orbitals’ approach to electronic communicability in macromolecular chains , 2007, 0905.4099.
[55] Maykel Pérez González,et al. A topological sub-structural approach for predicting human intestinal absorption of drugs. , 2004, European journal of medicinal chemistry.
[56] Humberto González-Díaz,et al. Alignment-free prediction of polygalacturonases with pseudofolding topological indices: experimental isolation from Coffea arabica and prediction of a new sequence. , 2009, Journal of proteome research.
[57] Ernesto Estrada,et al. In Silico Studies toward the Discovery of New Anti-HIV Nucleoside Compounds through the Use of TOPS-MODE and 2D/3D Connectivity Indices. 2. Purine Derivatives , 2005, J. Chem. Inf. Model..
[58] E Estrada. On the Topological Sub-Structural Molecular Design (TOSS-MODE) in QSPR/QSAR and Drug Design Research , 2000, SAR and QSAR in environmental research.
[59] Saul G. Jacchieri,et al. Mining combinatorial data in protein sequences and structures , 2004, Molecular Diversity.
[60] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[61] E Uriarte,et al. Recent advances on the role of topological indices in drug discovery research. , 2001, Current medicinal chemistry.
[62] Léon Personnaz,et al. On Cross Validation for Model Selection , 1999, Neural Computation.