Juan Fernández‐Recio

Consejo Superior de Investigaciones Científicas

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Brian Jiménez‐García

Energy Transitions (United Kingdom)

Iain H. Moal

Age UK

Carles Pons

Barcelona Institute for Science and Technology

Laura Pérez‐Cano

University of California, Los Angeles

Mireia Rosell

Universidad de La Rioja

LÁ

Luis Ángel Rodríguez-Lumbreras

Instituto de Ciencias de la Vid y del Vino

Chiara Pallara

University of Bari Aldo Moro

Paul A. Bates

The Francis Crick Institute

Miguel Romero‐Durana

Universitat Politècnica de Catalunya

Alexandre M. J. J. Bonvin

Utrecht University

Cooperative Institutions

Universitat de Barcelona

Centre National de la Recherche Scientifique

Universitat Politècnica de Catalunya

Hospital Universitari Germans Trias i Pujol

Consejo Superior de Investigaciones Científicas

Institute for Research in Biomedicine

Barcelona Supercomputing Center

Centro de Investigación Biomédica en Red de Enfermedades Respiratorias

Centro de Investigación en Red en Enfermedades Cardiovasculares

Universitat Autònoma de Barcelona

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Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems

Advances in protein chemistry and structural biology (2017)

Didier Barradas‐Bautista Mireia Rosell Chiara Pallara Juan Fernández‐Recio

Docking (animal)

Protein–ligand docking

Macromolecular docking

10.1016/bs.apcsb.2017.06.003

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Citations (21)

SwarmDock: a server for flexible protein–protein docking

Bioinformatics (2013)

Mieczyslaw Torchala Iain H. Moal Raphaël A. G. Chaleil Juan Fernández‐Recio Paul A. Bates

Abstract Summary: Protein–protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein–protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available. Availability: The server is freely available and can be accessed at: http://bmm.cancerresearchuk.org/%7ESwarmDock/. Contact: Paul.Bates@cancer.org.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Docking (animal)

Upload

Macromolecular docking

10.1093/bioinformatics/btt038

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Citations (277)

La supercomputación: una poderosa herramienta para la investigación en bioquímica y biología molecular

Juan Fernández‐Recio

10.18567/sebbmdiv_rpc.2016.02.1

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Citations (0)

Structural and energy determinants in protein-RNA docking

Methods (2016)

Laura Pérez‐Cano Miguel Romero‐Durana Juan Fernández‐Recio

Docking (animal)

Protein–ligand docking

Macromolecular docking

10.1016/j.ymeth.2016.11.001

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Citations (18)

The pyDock interface scoring functions

Luis Ángel Rodríguez-Lumbreras Mireia Ginestí Rosell Miguel Romero‐Durana Juan Fernández‐Recio

Trabajo presentado en el 3D-Bioinformatics 2020 Annual Workshop, celebrado online del 24 al 26 de noviembre de 2020

Interface (matter)

Source

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Citations (0)

New Efficient Substrates for Semicarbazide-Sensitive Amine Oxidase/VAP-1 Enzyme: Analysis by SARs and Computational Docking

Journal of Medicinal Chemistry (2006)

Francesc Yraola Silvia García‐Vicente Juan Fernández‐Recio Fernando Alberício António Zorzano

Structure activity relationships for semicarbazide-sensitive amine oxidase/vascular adhesion protein-1 (SSAO/VAP-1) were studied using a library of arylalkylamine substrates, with the aim of contributing to the discovery of more efficient SSAO substrates. Experimental data were contrasted with computational docking studies, thereby allowing us to examine the mechanism and substrate-binding affinity of SSAO and thus contribute to the discovery of more efficient SSAO substrates and provide a structural basis for their interactions. We also built a model of the mouse SSAO structure, which provides several structural rationales for interspecies differences in SSAO substrate selectivity and reveals new trends in SSAO substrate recognition. In this context, we identified novel efficient substrates for human SSAO that can be used as a lead for the discovery of antidiabetic agents.

Docking (animal)

Semicarbazide

Amine oxidase (copper-containing)

10.1021/jm051076e

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Citations (34)

SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

Bioinformatics (2018)

Justina Jankauskaitė Brian Jiménez‐García Justas Dapkūnas Juan Fernández‐Recio Iain H. Moal

Abstract Motivation Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. Results We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. This version now contains manually curated binding data for 7085 mutations, an increase of 133%, including changes in kinetics for 1844 mutations, enthalpy and entropy changes for 443 mutations, and 440 mutations, which abolish detectable binding. Availability and implementation The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary information Supplementary data are available at Bioinformatics online.

Protein Data Bank

10.1093/bioinformatics/bty635

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Citations (262)

L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction

Nature Communications (2019)

Ekaitz Errasti‐Murugarren Joana Fort Paola Bartoccioni Lucía Díaz Els Pardon

L-amino acid transporters (LATs) play key roles in human physiology and are implicated in several human pathologies. LATs are asymmetric amino acid exchangers where the low apparent affinity cytoplasmic side controls the exchange of substrates with high apparent affinity on the extracellular side. Here, we report the crystal structures of an LAT, the bacterial alanine-serine-cysteine exchanger (BasC), in a non-occluded inward-facing conformation in both apo and substrate-bound states. We crystallized BasC in complex with a nanobody, which blocks the transporter from the intracellular side, thus unveiling the sidedness of the substrate interaction of BasC. Two conserved residues in human LATs, Tyr 236 and Lys 154, are located in equivalent positions to the Na1 and Na2 sites of sodium-dependent APC superfamily transporters. Functional studies and molecular dynamics (MD) calculations reveal that these residues are key for the asymmetric substrate interaction of BasC and in the homologous human transporter Asc-1.

10.1038/s41467-019-09837-z

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Citations (72)

Docking analysis of transient complexes: Interaction of ferredoxin‐NADP⁺ reductase with ferredoxin and flavodoxin

Proteins Structure Function and Bioinformatics (2008)

Milagros Medina Ruben Abagyan Carlos Gómez‐Moreno Juan Fernández‐Recio

Abstract Ferredoxin (Fd) interacts with ferredoxin‐NADP + reductase (FNR) to transfer two electrons to the latter, one by one, which will finally be used to reduce NADP + to NADPH. The formation of a transient complex between Fd and FNR is required for the electron transfer (ET), and extensive mutational and crystallographic studies have been reported to characterize such protein–protein interaction. However, some aspects of the association mechanism still remain unclear. Moreover, in spite of their structural differences, flavodoxin (Fld) can replace Fd in its function and interact with FNR to transfer electrons with only slightly lower efficiency. Although crystallographic structures for the FNR:Fd association have been reported, experimental structural data for the FNR:Fld interaction are highly elusive. We have modeled here the interactions between FNR and both of its protein partners, Fd and Fld, using surface energy analysis, computational rigid‐body docking simulations, and interface side‐chain refinement. The results, consistent with previous experimental data, suggest the existence of alternative binding modes in these ET proteins. Proteins 2008. © 2008 Wiley‐Liss, Inc.

Flavodoxin

Ferredoxin—NADP(+) reductase

Docking (animal)

10.1002/prot.21979

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Citations (27)

Efficient Restraints for Protein–Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment

Journal of Molecular Biology (2006)

Vijayalakshmi Chelliah Tom L. Blundell Juan Fernández‐Recio

Docking (animal)

Macromolecular docking

10.1016/j.jmb.2006.01.001

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Citations (66)