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Results: 265
Implications of AlphaFold2 for crystallographic phasing by molecular replacement.
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether...
Structure of a 13-fold superhelix (almost) determined from first principles.
Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor...
Macromolecular ab initio phasing enforcing secondary and tertiary structure.
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main...
Evaluation of template-based modeling in CASP13.
Performance in the template-based modeling (TBM) category of CASP13 is assessed here, using a variety of metrics. Performance of the predictor groups that participated is ranked using the primary ranking score that was developed...
ALEPH
Ana Medina, Josep Triviño, Rafael J Borges, Claudia Millán, Isabel Usón, Massimo D Sammito
Apr 05, 2020
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where...
Implications of AlphaFold2 for crystallographic phasing by molecular replacement.
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether...
ALEPH
Ana Medina, Josep Triviño, Rafael J Borges, Claudia Millán, Isabel Usón, Massimo D Sammito
Apr 27, 2020
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where...
Gyre and gimble
Airlie J McCoy, Robert D Oeffner, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J Read
Oct 10, 2018
Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified...
Detection of translational noncrystallographic symmetry in Patterson functions.
Iracema Caballero, Massimo D Sammito, Pavel V Afonine, Isabel Usón, Randy J Read, Airlie J McCoy
Jan 11, 2021
Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the...
Factors influencing estimates of coordinate error for molecular replacement.
Good prior estimates of the effective root-mean-square deviation (r.m.s.d.) between the atomic coordinates of the model and the target optimize the signal in molecular replacement, thereby increasing the success rate in...
ARCIMBOLDO on coiled coils.
Iracema Caballero, Massimo Sammito, Claudia Millán, Andrey Lebedev, Nicolas Soler, Isabel Usón
Feb 19, 2021
ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be...
Factors influencing estimates of coordinate error for molecular replacement.
Good prior estimates of the effective root-mean-square deviation (r.m.s.d.) between the atomic coordinates of the model and the target optimize the signal in molecular replacement, thereby increasing the success rate in...
SEQUENCE SLIDER
Rafael Junqueira Borges, Kathrin Meindl, Josep Triviño, Massimo Sammito, Ana Medina, Claudia Millán, Martin Alcorlo, Juan A Hermoso, Marcos Roberto de Mattos Fontes, Isabel Usón
Apr 05, 2020
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser...
Phasertng
Airlie J McCoy, Duncan H Stockwell, Massimo D Sammito, Robert D Oeffner, Kaushik S Hatti, Tristan I Croll, Randy J Read
Jan 25, 2021
Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a...
SEQUENCE SLIDER
Rafael Junqueira Borges, Kathrin Meindl, Josep Triviño, Massimo Sammito, Ana Medina, Claudia Millán, Martin Alcorlo, Juan A Hermoso, Marcos Roberto de Mattos Fontes, Isabel Usón
Apr 06, 2020
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser...
Assessing the utility of CASP14 models for molecular replacement.
Claudia Millán, Ronan M Keegan, Joana Pereira, Massimo D Sammito, Adam J Simpkin, Airlie J McCoy, Andrei N Lupas, Marcus D Hartmann, Daniel J Rigden, Randy J Read
Aug 09, 2021
The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real-world application. In CASP7, the metric for molecular replacement assessment involved full likelihood-based...
Assessing the utility of CASP14 models for molecular replacement
Claudia Millán, Ronan M. Keegan, Joana Pereira, Massimo D. Sammito, Adam J. Simpkin, Airlie J. McCoy, Andrei N. Lupas, Marcus D. Hartmann, Daniel J. Rigden, Randy J. Read
Aug 26, 2021
RESEARCH ARTICLE RESEARCH ARTICLES CASP likelihood model refinement Molecular replacement structure prediction
Published by: John Wiley & Sons, Inc.
Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.
Claudia Millán, Massimo Domenico Sammito, Airlie J McCoy, Andrey F Ziem Nascimento, Giovanna Petrillo, Robert D Oeffner, Teresa Domínguez-Gil, Juan A Hermoso, Randy J Read, Isabel Usón
Jul 04, 2018
Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an...
Mitochondrial complex III Rieske Fe-S protein processing and assembly.
Regulation of the mitochondrial respiratory chain biogenesis is a matter of great interest because of its implications for mitochondrial disease. One of the mitochondrial disease genes recently discovered associated to...
mitochondrial respiratory chain OXPHOS Rieske Fe-S protein TTC19 UQCRFS1 Mitochondria mitochondrial complex III mitochondrial disease Animals Cattle Chickens Electron Transport Complex III Membrane Proteins Mice Mice Knockout Mitochondria Mitochondrial Proteins Protein Binding Protein Structure Quaternary Protein Subunits
On the relationship between firms and their legal environment
In this study we seek to reconcile diverging dominant views on the relationship between firms and their legal environment by offering a cultural contingency perspective.
We begin by accepting the notion that a new law will...
We begin by accepting the notion that a new law will...
Introduction
Funder: Università degli Studi Roma Tre
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