Search Results - "Ortiz, Angel R"

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison by Ortiz, Angel R., Strauss, Charlie E.M., Olmea, Osvaldo

“…Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective, and well benchmarked methods capable of…”
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Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation by Scheper, Johanna, Guerra-Rebollo, Marta, Sanclimens, Glòria, Moure, Alejandra, Masip, Isabel, González-Ruiz, Domingo, Rubio, Nuria, Crosas, Bernat, Meca-Cortés, Oscar, Loukili, Noureddine, Plans, Vanessa, Morreale, Antonio, Blanco, Jerónimo, Ortiz, Angel R, Messeguer, Angel, Thomson, Timothy M

“…Several pathways that control cell survival under stress, namely RNF8-dependent DNA damage recognition and repair, PCNA-dependent DNA damage tolerance and…”
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An Analysis of Core Deformations in Protein Superfamilies by Leo-Macias, Alejandra, Lopez-Romero, Pedro, Lupyan, Dmitry, Zerbino, Daniel, Ortiz, Angel R.

“…An analysis is presented on how structural cores modify their shape across homologous proteins, and whether or not a relationship exists between these…”
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Improvement of Comparative Model Accuracy by Free-Energy Optimization along Principal Components of Natural Structural Variation by Qian, Bin, Ortiz, Angel R., Baker, David, Levitt, Michael

“…Accurate high-resolution refinement of protein structure models is a formidable challenge because of the delicate balance of forces in the native state, the…”
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Comparative Binding Energy Analysis Considering Multiple Receptors:  A Step toward 3D-QSAR Models for Multiple Targets by Murcia, Marta, Morreale, Antonio, Ortiz, Angel R

“…Comparative binding energy analysis, a technique to derive receptor-based three-dimensional quantitative structure−activity relationships (3D-QSAR), is herein…”
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CAFASP3: The third critical assessment of fully automated structure prediction methods by Fischer, Daniel, Rychlewski, Leszek, Dunbrack Jr, Roland L., Ortiz, Angel R., Elofsson, Arne

“…We present the results of the fully automated CAFASP3 experiment, which was carried out in parallel with CASP5, using the same set of prediction targets…”
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Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns by De Las Rivas, Javier, Lozano, Juan Jose, Ortiz, Angel R

“…All protein sequences from 19 complete chloroplast genomes (cpDNA) have been studied using a new computational method able to analyze functional correlations…”
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Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors:  Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design by Pérez, Carlos, Pastor, Manuel, Ortiz, Angel R, Gago, Federico

“…A comparative binding energy (COMBINE) analysis (Ortiz et al. J. Med. Chem. 1995, 38, 2681−2691) has been performed on a training set of 33 HIV-1 protease…”
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Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis by Ortiz, Angel R, Pisabarro, M. Teresa, Gago, Federico, Wade, Rebecca C

“…A new computational method for deducing quantitative structure-activity relationships (QSARs) using structural data from ligand-macromolecule complexes is…”
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Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two‐layer sandwich architecture by León, Esther, Yee, Adelinda, Ortíz, Angel R., Santoro, Jorge, Rico, Manuel, Jiménez, M. Angeles

“…TA0095 is a 96‐residue hypothetical protein from Thermoplasma acidophilum that exhibits no sequence similarity to any protein of known structure. Also, TA0095…”
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A new progressive-iterative algorithm for multiple structure alignment by Lupyan, Dmitry, Leo-Macias, Alejandra, Ortiz, Angel R.

“…Motivation: Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of…”
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Nativelike Topology Assembly of Small Proteins Using Predicted Restraints in Monte Carlo Folding Simulations by Ortiz, Angel R., Kolinski, Andrzej, Skolnick, Jeffrey

“…By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible…”
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Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data by Lozano, Juan Jose, Soler, Marta, Bermudo, Raquel, Abia, David, Fernandez, Pedro L, Thomson, Timothy M, Ortiz, Angel R

“…We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant…”
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Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence:  Application to the Small Protein CMTI-1 by Simmerling, Carlos, Lee, Matthew R, Ortiz, Angel. R, Kolinski, Andrzej, Skolnick, Jeffrey, Kollman, Peter A

“…A combined method for the prediction of protein tertiary structures from sequence is presented. This multistep procedure initially uses a simplified approach…”
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Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures by Pascual-García, Alberto, Abia, David, Ortiz, Angel R, Bastolla, Ugo

“…Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which…”
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Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors by Murcia, Marta, Ortiz, Angel R

“…A two-step, fully automatic virtual screening procedure consisting of flexible docking followed by activity prediction by COMparative BINding Energy (COMBINE)…”
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Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities by Ruiz, Federico M, Gil-Redondo, Rubén, Morreale, Antonio, Ortiz, Ángel R, Fábrega, Carmen, Bravo, Jerónimo

“…The human DNA-repair O6-alkylguanine DNA alkyltransferase (MGMT or hAGT) protein protects DNA from environmental alkylating agents and also plays an important…”
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Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences by Bastolla, Ugo, Ortíz, Angel R., Porto, Markus, Teichert, Florian

“…The complexity of protein structures calls for simplified representations of their topology. The simplest possible mathematical description of a protein…”
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A new implicit solvent model for protein-ligand docking by Morreale, Antonio, Gil-Redondo, Rubén, Ortiz, Ángel R.

“…A new implicit solvent model for computing the electrostatics binding free energy in protein–ligand docking is proposed. The new method is based on an…”
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An efficient conformational sampling method for homology modeling by Han, Rongsheng, Leo-Macias, Alejandra, Zerbino, Daniel, Bastolla, Ugo, Contreras-Moreira, Bruno, Ortiz, Angel R.

“…The structural refinement of protein models is a challenging problem in protein structure prediction (Moult et al., Proteins 2003;53(Suppl 6):334–339). Most…”
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