Modeling chromatographic parameters by a novel graph theoretical sub-structural approachE Estrada
Department of Pharmacy, Faculty of Chemistry and Pharmacy, Universidad Central de Las Villas, Villa Clara, Cuba
J Chromatogr A 858:187-99. 1999
..The physicochemical interpretation of the results on the basis of the retention mechanisms is also analyzed in light of this new approach...
- A novel approach for the virtual screening and rational design of anticancer compounds
E Estrada
Faculty of Pharmacy, Department of Organic Chemistry, Universidad de Santiago de Compostela, 15706 Santiago de Compostela, Spain
J Med Chem 43:1975-85. 2000
..The chloropurine derivatives were the most active compounds, especially compounds 6c, d...
- Molecular modeling (MM2 and PM3) and experimental (NMR and thermal analysis) studies on the inclusion complex of salbutamol and beta-cyclodextrin
E Estrada
Department of Organic Chemistry and Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
J Org Chem 65:8510-7. 2000
..The solid-state complex was prepared and its stoichiometry (beta-CD.C(13)H(21)NO(3).8H(2)O) and dissociation process studied by thermogravimetric analysis...
- Protein bipartivity and essentiality in the yeast protein-protein interaction network
Ernesto Estrada
Complex System Research Group, X rays Unit, RIAIDT, University of Santiago de Compostela, Edificio CACTUS, Santiago de Compostela 15782, Spain
J Proteome Res 5:2177-84. 2006
..Consequently, these new replicas evolving from nonbipartite (essential) targets will with high probability be essential...
- Using network centrality measures to manage landscape connectivity
Ernesto Estrada
Complex Systems Research Group, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
Ecol Appl 18:1810-25. 2008
..This finding may enable multispecies analyses of single-species network models...
- Characterization of the amino acid contribution to the folding degree of proteins
Ernesto Estrada
Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Beds, and RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain
Proteins 54:727-37. 2004
..These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach...
- A protein folding degree measure and its dependence on crystal packing, protein size, secondary structure, and domain structural class
Ernesto Estrada
Molecular Informatics, X Ray Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
J Chem Inf Comput Sci 44:1238-50. 2004
..Automating the classification of proteins into their respective structural domain classes, namely mainly-alpha, mainly-beta, and alpha-beta, is also possible...
- How the parts organize in the whole? A top-down view of molecular descriptors and properties for QSAR and drug design
Ernesto Estrada
Complex Systems Research Group, X Ray Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
Mini Rev Med Chem 8:213-21. 2008
....
- Folding degrees of azurins and pseudoazurins. Implications for structure and function
Ernesto Estrada
Complex Systems Research Group, X Ray Unit, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
Comput Biol Chem 29:345-53. 2005
..However, it is only able to explain less than 75% in the variance of the reduction potential of these proteins instead of the 95% explained by the folding degree of His117...
- Virtual identification of essential proteins within the protein interaction network of yeast
Ernesto Estrada
Complex Systems Research Group, X Ray Unit, RIAIDT, University of Santiago de Compostela, Edificio CACTUS, Santiago de Compostela 15782, Spain
Proteomics 6:35-40. 2006
..Subgraph centrality gives important structural information about the role of individual proteins, and permits the selection of possible targets for rational drug discovery through the identification of essential proteins in the PIN...
- Effect of protein backbone folding on the stability of protein-ligand complexes
Ernesto Estrada
Complex Systems Research Group, X Ray Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
J Proteome Res 5:105-11. 2006
..This study provides a basis for further consideration of the degree of folding as a parameter for empirical structural parametrizations of the binding energetics of protein folding and binding...
- Tight-binding "dihedral orbitals" approach to the degree of folding of macromolecular chains
Ernesto Estrada
Complex Systems Research Group, X rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
J Phys Chem B 111:13611-8. 2007
..Finally, we illustrate the use of the dihedral energy and the partition function in structure-property studies of proteins by analyzing the binding of steroids to DB3 antibody...
- Automatic extraction of structural alerts for predicting chromosome aberrations of organic compounds
Ernesto Estrada
Complex Systems Research Group, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
J Mol Graph Model 25:275-88. 2006
..The chemico-biological analysis of some of the structural alerts found is also carried out showing the potential of TOPS-MODE as a knowledge generator...
- Food webs robustness to biodiversity loss: the roles of connectance, expansibility and degree distribution
Ernesto Estrada
Complex Systems Research Group, X rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Santiago de Compostela, Spain
J Theor Biol 244:296-307. 2007
....
- An integrated in silico analysis of drug-binding to human serum albumin
Ernesto Estrada
Complex Systems Research Group, X rays Unit, Edificio CACTUS, Santiago de Compostela 15982, Spain
J Chem Inf Model 46:2709-24. 2006
..A small number of fragments appear very frequently in most drugs. These molecular "empathic" fragments are good candidates for guiding future drug discovery research...
- Creating molecular diversity from antioxidants in Brazilian propolis. Combination of TOPS-MODE QSAR and virtual structure generation
Ernesto Estrada
Safety, and Environmental Assurance Centre SEAC, Unilever Colworth, Sharnbrook, Bedford, UK
Mol Divers 8:21-33. 2004
..This contributes to enhance the molecular diversity of the analogues of Brazilian propolis compounds with antioxidative properties...
- Computer-aided knowledge generation for understanding skin sensitization mechanisms: the TOPS-MODE approach
Ernesto Estrada
Safety and Environmental Assurance Centre SEAC, Unilever Colworth, Colworth House, Sharnbrook, Bedford, MK44 1LQ, United Kingdom
Chem Res Toxicol 16:1226-35. 2003
..The models have also been able to identify potential structural alerts for chemicals requiring metabolic activation...
- Application of a novel graph-theoretic folding degree index to the study of steroid-DB3 antibody binding affinity
Ernesto Estrada
Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
Comput Biol Chem 27:305-13. 2003
..This study shows the possibilities of application for the graph-theoretic folding degree index in studying drug-protein interactions...
- In silico studies for the rational discovery of anticonvulsant compounds
E Estrada
Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Spain
Bioorg Med Chem 8:2755-70. 2000
..Some structure-anticonvulsant activity relationships are derived on the basis of the 3-D structure of this fragment and some findings reported in the literature that indicate that it is an important pharamacophore are outlined...
- Recent advances on the role of topological indices in drug discovery research
E Estrada
Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
Curr Med Chem 8:1573-88. 2001
..Future outlooks of development in this area of research are also given...
- Quantum-chemical foundations of the topological substructural molecular design
Ernesto Estrada
Complex Systems Research Group, RIAIDT and Department of Organic Chemistry, Faculty of Pharmacy, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
J Phys Chem A 112:5208-17. 2008
....
- Novel local (fragment-based) topological molecular descriptors for QSpr/QSAR and molecular design
E Estrada
Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Spain
J Mol Graph Model 20:54-64. 2001
..98) was obtained with these group contributions with Hammett sigma(p) constants for 21 groups...
- Quantitative structure-toxicity relationships using TOPS-MODE. 2. Neurotoxicity of a non-congeneric series of solvents
E Estrada
Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Spain
SAR QSAR Environ Res 12:445-59. 2001
..The differences in neurotoxic behavior of some fragments in rats and mice were also analyzed, which could give insights on the toxicological mechanism of action of solvents studied...
- Characterization of the folding degree of proteins
Ernesto Estrada
Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
Bioinformatics 18:697-704. 2002
..Here we present a new index for characterizing the folding degree of a (protein) chain. This index shows a range of features that are desirable for the study of the relation between structure and function in proteins...
- 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
Ernesto Estrada
Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
J Chem Inf Comput Sci 42:1194-203. 2002
..The combination of both models will permit the selection of pyrimidyl nucleoside leads and their optimization to improve the potency of the selected ones...
- Quantitative structure-toxicity relationships using TOPS-MODE. 3. Structural factors influencing the permeability of commercial solvents through living human skin
E Estrada
Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
SAR QSAR Environ Res 14:145-63. 2003
..Drawing on the idea of permeability "enhancers" and "inhibitors", we hypothesized that the solvents needed to orientate themselves in front of the stratum corneum layer first before penetrating through the skin...
- Point scattering: a new geometric invariant with applications from (nano)clusters to biomolecules
Ernesto Estrada
Complex Systems Research Group, X Ray Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
J Comput Chem 28:767-77. 2007
..Point scattering also shows better correlation with thermodynamic parameters of binding and describes the interior cavities of hollowed ensembles better than the other geometric measures...
- 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
Santiago Vilar
Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
J Chem Inf Model 45:502-14. 2005
..Finally, a QSAR model has been developed that allows quantitative data to be obtained regarding the pharmacological potency shown by this type of compound...
- Order from chaos: observing hormesis at the proteome level
Milan Randić
Complex Systems Research Group, X rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain
J Proteome Res 4:2133-6. 2005
..The work is based on the available data of Anderson at al. on the effects of peroxisome proliferator LY171883 on protein abundances in mouse liver when administrated at different concentrations...
- Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors
Ernesto Estrada
Complex Systems Research Group, X-rays Unit, RIAIDT, Edificio CACTUS, University of Santiago of Compostela, 15782, Santiago de Compostela, Spain
J Comput Aided Mol Des 20:539-48. 2006
..The current models allow a more transparent physical interpretation of the phenomenon in terms of intermolecular interactions which occur in solution and which explain the respective deviations from ideality...
- Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach
E Estrada
Department of Drug Design, Centro de Bioactivos Químicos, Universidad Central de Las Villas, Villa Clara, Cuba
J Comput Aided Mol Des 12:583-95. 1998
..Several compounds from the Merck Index were identified by the model as sedative/hypnotic, five of them were found in the recent literature as possessing this activity. The critical fragments, actives and inactive ones, were detected...
- Quantitative structure--toxicity relationships using TOPS-MODE. 1. Nitrobenzene toxicity to Tetrahymena pyriformis
E Estrada
Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
SAR QSAR Environ Res 12:309-24. 2001
..TOPS-MODE was used to derive the contribution of different fragments to the toxicity of studied compounds. These contributions were applied to calculate toxicity substituent constants for the groups present in the nitrobenzenes studied...
- A modelling assessment of the atmospheric fate of volatile methyl siloxanes and their reaction products
M J Whelan
Unilever Colworth Laboratory, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
Chemosphere 57:1427-37. 2004
..Predictions of silanol hydrolysis in liquid water droplets suggest that the mix of diol chain lengths in precipitation may not be in thermodynamic equilibrium and will depend on atmospheric residence time and pH...
- Synthesis of compounds with antiproliferative activity as analogues of prenylated natural products existing in Brazilian propolis
Laura Pisco
, , UNIBAN, Vila Guilherme, Brazil
Eur J Med Chem 41:401-7. 2006
..The compounds were tested for their cytotoxicity toward a diverse panel of cultured human tumor cell lines. Compound 3 showed significant selective cytotoxic activity (IC(50) < 9 microg/ml)...
