B. Jiménez-García

发表

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Raphael A. G. Chaleil, Z. Weng, J. Fernández-Recio, 2015, Journal of molecular biology.

Blind prediction of interfacial water positions in CAPRI

Kengo Kinoshita, Haruki Nakamura, Xiaoqin Zou, 2014, Proteins.

Towards design of drugs and delivery systems with the Martini coarse-grained model

Paulo C. T. Souza, M. Cecchini, B. Jiménez-García, 2022, QRB Discovery.

pyDockDNA: A new web server for energy-based protein-DNA docking and scoring

J. Fernández-Recio, B. Jiménez-García, Silvia Giménez-Santamarina, 2022, Frontiers in Molecular Biosciences.

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring

Carles Pons, Juan Fernández-Recio, Brian Jiménez-García, 2013, Bioinform..

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Antonio Rosato, Andrea Giachetti, Panagiotis I. Koukos, 2021, Frontiers in Molecular Biosciences.

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking

F. Ambrosetti, T. H. Olsen, P. P. Olimpieri, 2020, bioRxiv.

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

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2018, bioRxiv.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Jeffrey J. Gray, Panagiotis I. Koukos, Johnathan D. Guest, 2021, Proteins.

Modeling Antibody-Antigen Complexes by Information-Driven Docking.

Alexandre M J J Bonvin, Brian Jiménez-García, Jorge Roel-Touris, 2019, Structure.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Integrative modeling of membrane-associated protein assemblies

Brian Jiménez-García, Jorge Roel-Touris, Alexandre M.J.J. Bonvin, 2020, Nature Communications.

LightDock goes information-driven

Alexandre M. J. J. Bonvin, Brian Jiménez-García, Jorge Roel-Touris, 2019, bioRxiv.

LightDock: a new multi-scale approach to protein–protein docking

Daniel Jiménez-González, Juan Fernández-Recio, Brian Jiménez-García, 2018, Bioinform..

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

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2018, bioRxiv.

Information-Driven Modelling of Antibody-Antigen Complexes

Alexandre M. J. J. Bonvin, Brian Jiménez-García, Jorge Roel-Touris, 2019, SSRN Electronic Journal.

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

Zhiping Weng, Mieczyslaw Torchala, Juan Fernández-Recio, 2017, Bioinform..

CCharPPI web server: computational characterization of protein-protein interactions from structure

Juan Fernández-Recio, Iain H. Moal, Brian Jiménez-García, 2015, Bioinform..

A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data

Laura Pérez-Cano, Juan Fernández-Recio, Brian Jiménez-García, 2012, Proteins.

pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions

Juan Fernández-Recio, Brian Jiménez-García, Chiara Pallara, 2017, Proteins.

Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking

Paulo C. T. Souza, B. Jiménez-García, G. Launay, 2023, bioRxiv.

MuGVRE. A virtual research environment for 3D/4D genomics

Rosa M. Badia, Javier Conejero, Ricard Illa, 2019, bioRxiv.

Structural Characterization of Protein-Protein Interactions with pyDockSAXS.

Juan Fernández-Recio, Brian Jiménez-García, Pau Bernadó, 2020, Methods in molecular biology.

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Charles W Christoffer, H. Wolfson, O. Schueler‐Furman, 2023, Proteomics.

Integrative modeling of protein‐protein interactions with pyDock for the new docking challenges

Brian Jiménez-García, Miguel Romero-Durana, Juan Fernandez-Recio, 2019, Proteins.

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes

Alexandre M J J Bonvin, Katarina Elez, Brian Jiménez-García, 2019, Bioinform..

pyDockEneRes: per-residue decomposition of protein-protein docking energy

Juan Fernández-Recio, Brian Jiménez-García, Miguel Romero-Durana, 2019, Bioinform..

Expanding the frontiers of protein–protein modeling: From docking and scoring to binding affinity predictions and other challenges

Solène Grosdidier, Albert Solernou, Laura Pérez-Cano, 2013, Proteins.

Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking

Paulo C. T. Souza, R. Pellarin, B. Jiménez-García, 2023, bioRxiv.