Electronic and Atomic Protein Modeling (EAPM)

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Mostrando 31 - 60 resultados de 173

2021

Structural basis for substrate specificity of heteromeric transporters of neutral amino acidsSignificance

Proceedings of the National Academy of Sciences

C. F. Rodriguez, P. Escudero-Bravo, L. Díaz, P. Bartoccioni, C. García-Martín, J. G. Gilabert, J. Boskovic, V. Guallar, E. Errasti-Murugarren, O. Llorca, and M. Palacín
Elucidation of ligand binding and dimerization of

Proteins: Structure, Function, and Bioinformatics

H. Sameer, G. Victor, S. Katalin, and A. Henrik
Structural-Based Modeling in Protein Engineering. A Must Do

The Journal of Physical Chemistry B

S. Roda, A. Robles-Martín, R. Xiang, M. Kazemi, and V. Guallar
Structural-Based Modeling in Protein Engineering. A Must Do

The Journal of Physical Chemistry B

S. Roda, A. Robles-Martín, R. Xiang, M. Kazemi, and V. Guallar
Comprehensive Insights into the Production of Long Chain Aliphatic Aldehydes Using a Copper-Radical Alcohol Oxidase as Biocatalys

ACS Sustainable Chemistry & Engineering

D. Ribeaucourt, B. Bissaro, V. Guallar, M. Yemloul, M. Haon, S. Grisel, V. Alphand, H. Brumer, F. Lambert, J-G. Berrin, and M. Lafond
Computationally Driven Rational Design of Substrate Promiscuity on Serine Ester Hydrolases

ACS Catalysis

S. Roda, L. Fernandez-Lopez, R. Cañadas, G. Santiago, M. Ferrer, and V. Guallar

2020

UEP: an open-source and fast classifier for predicting the impact of mutations in protein–protein complexesAbstractMotivationResultsAvailability and implementationSupplementary information

Bioinformatics

P. Amengual-Rigo, J. Fernández-Recio, and V. Guallar
aquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of Buried Water Molecules in Proteins

Journal of Chemical Theory and Computation

M. Municoy, S. Roda, D. Soler, A. Soutullo, and V. Guallar
FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design

Journal of Chemical Information and Modeling

C. Perez, D. Soler, R. Soliva, and V. Guallar
Sequential oxidation of 5-hydroxymethylfurfural to furan-2,5-dicarboxylic acid by an evolved aryl-alcohol oxidase

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

J. Viña-González, A. T. Martínez, V. Guallar, and M. Alcalde

2018

CHAPTER 10. Modeling O2-dependent Heme Enzymes: A Quick Guide for Non-experts

Dioxygen-dependent Heme Enzymes

F. Sancho, G. Santiago, P. Amengual-Rigo, and V. Guallar
Kauniolide synthase is a P450 with unusual hydroxylation and cyclization-elimination activity

Nature Communications

Q. Liu, A. Beyraghdar Kashkooli, D. Manzano, I. Pateraki, L. Richard, P. Kolkman, M F. Lucas, V. Guallar, R. C. H. de Vos, M. C. R. Franssen, A. van der Krol, and H. Bouwmeester
Automated Design of Efficient and Functionally Diverse Enzyme Repertoires

Molecular Cell

O. Khersonsky, R. Lipsh, Z. Avizemer, iv, Y. Ashani, M. Goldsmith, H. Leader, O. Dym, S. Rogotner, D. L. Trudeau, J. Prilusky, P. Amengual-Rigo, V. Guallar, D. S. Tawfik, and S. J. Fleishman
Description of a Non-Canonical Mn(II)-Oxidation Site in Peroxidases

ACS Catalysis

E. Fernández-Fueyo, I. Davó-Siguero, D. Almendral, D. Linde, M C. Baratto, R. Pogni, A. Romero, V. Guallar, and A. T. Martínez
Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case

Journal of Chemical Information and Modeling

M. Kotev, R. Pascual, C. Almansa, V. Guallar, and R. Soliva
Multiple implications of an active site phenylalanine in the catalysis of aryl-alcohol oxidase

Scientific Reports

J. Carro, P. Amengual-Rigo, F. Sancho, M. Medina, V. Guallar, P. Ferreira, and A. T. Martínez
Computational structure-based drug design: Predicting target flexibility

Wiley Interdisciplinary Reviews: Computational Molecular Science

J. Iglesias, S. Saen-oon, R. Soliva, and V. Guallar
Selective Synthesis of the Human Drug Metabolite 5′-Hydroxypropranolol by an Evolved Self-Sufficient Peroxygenase

ACS Catalysis

P. Gomezde Santos, M. Cañellas, F. Tieves, S. H. H. Younes, P. Molina-Espeja, M. Hofrichter, F. Hollmann, V. Guallar, and M. Alcalde
Rational Engineering of Multiple Active Sites in an Ester Hydrolase

Biochemistry

G. Santiago, M. Martínez-Martínez, S. Alonso, R. Bargiela, C. Coscolín, P. N. Golyshin, V. Guallar, and M. Ferrer

2017

Determinants and Prediction of Esterase Substrate Promiscuity Patterns

ACS Chemical Biology

M. Martínez-Martínez, C. Coscolín, G. Santiago, J. Chow, P. J. Stogios, R. Bargiela, C. Gertler, J. Navarro-Fernández, A. Bollinger, S. Thies, C. Méndez-García, A. Popovic, G. Brown, T. N. Chernikova, A. García-Moyano, G. E. K. Bjerga, P. Pérez-García, T. Hai, M. V. Del Pozo, R. Stokke, I. H. Steen, H. Cui, X. Xu, B. P. Nocek, M. Alcaide, M. Distaso, V. Mesa, A. I. Peláez, J. Sánchez, P. C. F. Buchholz, J. Pleiss, A. Fernández-Guerra, F. O. Glöckner, O. V. Golyshina, M. M. Yakimov, A. Savchenko, K-E. Jaeger, A. F. Yakunin, W. R. Streit, P. N. Golyshin, V. Guallar, M. Ferrer, and T. I. N. M. A. R. E. Consortium
Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils

The Journal of Physical Chemistry B

F. Peccati, S. Pantaleone, V. Riffet, X. Solans-Monfort, J. Contreras-García, V. Guallar, and M. Sodupe
The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths

PLOS Computational Biology

G. Gygli, M F. Lucas, V. Guallar, and W. J. H. van Berkel
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs

Journal of Chemical Information and Modeling

M. Kotev, P. Manuel-Manresa, E. Hernando, V. Soto-Cerrato, M. Orozco, R. Quesada, R. Pérez-Tomás, and V. Guallar
Adaptive simulations, towards interactive protein-ligand modeling

Scientific Reports

D. Lecina, J. F. Gilabert, and V. Guallar
Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

Directed Enzyme Evolution: Advances and Applications

E. Monza, S. Acebes, M F. Lucas, and V. Guallar
Physics-Based Visual Characterization of Molecular Interaction Forces

IEEE Transactions on Visualization and Computer Graphics

P. Hermosilla, J. Estrada, V. Guallar, T. Ropinski, A. Vinacua, and P-P. Vázquez
Repurposing designed mutants: a valuable strategy for computer-aided laccase engineering – the case of POXA1b

Catalysis Science & Technology

V. GuidoGiacobelli, E. Monza, F. M. Lucas, C. Pezzella, A. Piscitelli, V. Guallar, and G. Sannia
Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

The Journal of Physical Chemistry B

S. Acebes, F. J. Ruiz-Due?as, M. Toubes, V. S?ez-Jim?nez, M. P?rez-Boada, M.. F.?tima Lucas, A. T. Mart?nez, and V. Guallar
Interactive GPU-based generation of solvent-excluded surfaces

The Visual Computer

P. Hermosilla, M. Krone, V. Guallar, P-P. V?zquez, ?lvar. Vinacua, and T. Ropinski
Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design

Journal of Chemical Theory and Computation

M F. Lucas, E. Monza, L. J. Jørgensen, H. A. Ernst, K. Piontek, M. J. Bjerrum, A. T. Martínez, S. Camarero, and V. Guallar

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