Search Results - "MARTIN, Osvaldo A"

PyMC: a modern, and comprehensive probabilistic programming framework in Python by Abril-Pla, Oriol, Andreani, Virgile, Carroll, Colin, Dong, Larry, Fonnesbeck, Christopher J, Kochurov, Maxim, Kumar, Ravin, Lao, Junpeng, Luhmann, Christian C, Martin, Osvaldo A, Osthege, Michael, Vieira, Ricardo, Wiecki, Thomas, Zinkov, Robert

“…PyMC is a probabilistic programming library for Python that provides tools for constructing and fitting Bayesian models. It offers an intuitive, readable…”
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Opportunities drive the global distribution of protected areas by Baldi, Germán, Texeira, Marcos, Martin, Osvaldo A, Grau, H Ricardo, Jobbágy, Esteban G

“…Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global…”
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Nature representation in South American protected areas: country contrasts and conservation priorities by Baldi, Germán, Schauman, Santiago, Texeira, Marcos, Marinaro, Sofía, Martin, Osvaldo A, Gandini, Patricia, Jobbágy, Esteban G

“…South America faces strong environmental pressures as a result of agriculture and infrastructure expansion and also of demographic growth, demanding immediate…”
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Accounting for a mirror-image conformation as a subtle effect in protein folding by Kachlishvili, Khatuna, Maisuradze, Gia G., Martin, Osvaldo A., Liwo, Adam, Vila, Jorge A., Scheraga, Harold A.

“…By using local (free-energy profiles along the amino acid sequence and 13Cα chemical shifts) and global (principal component) analyses to examine the molecular…”
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Classification of RNA backbone conformations into rotamers using 13C′ chemical shifts: exploring how far we can go by Icazatti, Alejandro A, Loyola, Juan M, Szleifer, Igal, Vila, Jorge A, Martin, Osvaldo A

“…The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone…”
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Outline of an experimental design aimed to detect a protein A mirror image in solution by Martin, Osvaldo A, Vorobjev, Yury, Scheraga, Harold A, Vila, Jorge A

“…There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such…”
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Physics-based method to validate and repair flaws in protein structures by Martin, Osvaldo A., Arnautova, Yelena A., Icazatti, Alejandro A., Scheraga, Harold A., Vila, Jorge A.

“…A method that makes use of information provided by the combination of ¹³C ᵅ and ¹³C ᵝ chemical shifts, computed at the density functional level of theory,…”
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Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study by Garay, Pablo G, Martin, Osvaldo A, Scheraga, Harold A, Vila, Jorge A

“…Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several…”
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A call for changing data analysis practices: from philosophy and comprehensive reporting to modeling approaches and back by Martin, Osvaldo A., Teste, François P.

“…Many applied disciplines have recognized problems related to the practice of data analysis within their own communities. Some of them have even declared the…”
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The Marginal Stability of Proteins: How the Jiggling and Wiggling of Atoms is Connected to Neutral Evolution by Martin, Osvaldo A., Vila, Jorge A.

“…Here we propose that the upper bound marginal stability of proteins is a universal property that includes macro-molecular complexes and is not affected by…”
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Bambi : A Simple Interface for Fitting Bayesian Linear Models in Python by Capretto, Tomás, Piho, Camen, Kumar, Ravin, Westfall, Jacob, Yarkoni, Tal, Martin, Osvaldo A.

“…The popularity of Bayesian statistical methods has increased dramatically in recent years across many research areas and industrial applications. This is the…”
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Exploring the quality of protein structural models from a Bayesian perspective by Arroyuelo, Agustina, Vila, Jorge A., Martin, Osvaldo A.

“…We explore how ideas and practices common in Bayesian modeling can be applied to help assess the quality of 3D protein structural models. The basic premise of…”
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Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules by Arroyuelo, Agustina, Vila, Jorge A., Martin, Osvaldo A.

“…Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of…”
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Assessing the One-Bond Cα–H Spin–Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches by Arroyuelo, Agustina, Martin, Osvaldo A, Scheraga, Harold A, Vila, Jorge A

“…In the present work, we explore three different approaches for the computation of the one-bond spin–spin coupling constants (SSCC) 1 J CαH in proteins: density…”
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Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation by Vila, Jorge A., Arnautova, Yelena A., Martin, Osvaldo A., Scheraga, Harold A.

“…A server ( Che Shift) has been developed to predict 13 C α chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a…”
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CheShift-2: graphic validation of protein structures by MARTIN, Osvaldo A, VILA, Jorge A, SCHERAGA, Harold A

“…The differences between observed and predicted (13)C(α) chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein…”
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Factors affecting the computation of the 13C shielding in disaccharides by Garay, Pablo G., Martin, Osvaldo A., Scheraga, Harold A., Vila, Jorge A.

“…Knowledge of the three‐dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are…”
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Are accurate computations of the 13C′ shielding feasible at the DFT level of theory? by Vila, Jorge A., Arnautova, Yelena A., Martin, Osvaldo A., Scheraga, Harold A.

“…The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the 13C′ shielding,…”
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Analysis of 13Cα and 13Cβ chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach by Martin, Osvaldo A, Villegas, Myriam E, Vila, Jorge A, Scheraga, Harold A

“…Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can…”
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Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study by Garay, Pablo G, Martin, Osvaldo A, Scheraga, Harold A, Vila, Jorge A

“…Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several…”
Get full text