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

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Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation von 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

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An Analysis of Core Deformations in Protein Superfamilies von Leo-Macias, Alejandra, Lopez-Romero, Pedro, Lupyan, Dmitry, Zerbino, Daniel, Ortiz, Angel R.

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Improvement of Comparative Model Accuracy by Free-Energy Optimization along Principal Components of Natural Structural Variation von Qian, Bin, Ortiz, Angel R., Baker, David, Levitt, Michael

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CAFASP3: The third critical assessment of fully automated structure prediction methods von Fischer, Daniel, Rychlewski, Leszek, Dunbrack Jr, Roland L., Ortiz, Angel R., Elofsson, Arne

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Comparative Binding Energy Analysis Considering Multiple Receptors:  A Step toward 3D-QSAR Models for Multiple Targets von Murcia, Marta, Morreale, Antonio, Ortiz, Angel R

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Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns von De Las Rivas, Javier, Lozano, Juan Jose, Ortiz, Angel R

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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 von Pérez, Carlos, Pastor, Manuel, Ortiz, Angel R, Gago, Federico

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Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis von Ortiz, Angel R, Pisabarro, M. Teresa, Gago, Federico, Wade, Rebecca C

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A new progressive-iterative algorithm for multiple structure alignment von Lupyan, Dmitry, Leo-Macias, Alejandra, Ortiz, Angel R.

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Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures von Pascual-García, Alberto, Abia, David, Ortiz, Angel R, Bastolla, Ugo

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Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two‐layer sandwich architecture von León, Esther, Yee, Adelinda, Ortíz, Angel R., Santoro, Jorge, Rico, Manuel, Jiménez, M. Angeles

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Nativelike Topology Assembly of Small Proteins Using Predicted Restraints in Monte Carlo Folding Simulations von Ortiz, Angel R., Kolinski, Andrzej, Skolnick, Jeffrey

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Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities von Ruiz, Federico M, Gil-Redondo, Rubén, Morreale, Antonio, Ortiz, Ángel R, Fábrega, Carmen, Bravo, Jerónimo

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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 von Lozano, Juan Jose, Soler, Marta, Bermudo, Raquel, Abia, David, Fernandez, Pedro L, Thomson, Timothy M, Ortiz, Angel R

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Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors von Murcia, Marta, Ortiz, Angel R

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A new implicit solvent model for protein-ligand docking von Morreale, Antonio, Gil-Redondo, Rubén, Ortiz, Ángel R.

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Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences von Bastolla, Ugo, Ortíz, Angel R., Porto, Markus, Teichert, Florian

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Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence:  Application to the Small Protein CMTI-1 von Simmerling, Carlos, Lee, Matthew R, Ortiz, Angel. R, Kolinski, Andrzej, Skolnick, Jeffrey, Kollman, Peter A

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VSDMIP: virtual screening data management on an integrated platform von Gil-Redondo, Rubén, Estrada, Jorge, Morreale, Antonio, Herranz, Fernando, Sancho, Javier, Ortiz, Ángel R.

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