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Optimization of protein-protein docking for predicting Fc-protein interactions.
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- Journal of Molecular Recognition, 2016, v. 29, n. 11, p. 555, doi. 10.1002/jmr.2555
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- Article
Exploring Molecular Contacts of MUC1 at CIN85 Binding Interface to Address Future Drug Design Efforts.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 4, p. 2208, doi. 10.3390/ijms22042208
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- Article
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces.
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- International Journal of Molecular Sciences, 2019, v. 20, n. 7, p. 1583, doi. 10.3390/ijms20071583
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Modelling the Evolution of COVID-19 in High-Incidence European Countries and Regions: Estimated Number of Infections and Impact of Past and Future Intervention Measures.
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- Journal of Clinical Medicine, 2020, v. 9, n. 6, p. 1825, doi. 10.3390/jcm9061825
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- Article
pyDockSAXS: protein--protein complex structure by SAXS and computational docking.
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- Nucleic Acids Research, 2015, v. 43, n. W1, p. W356, doi. 10.1093/nar/gkv368
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- Article
Conformational transitions in human translin enable nucleic acid binding.
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- Nucleic Acids Research, 2013, v. 41, n. 21, p. 9956, doi. 10.1093/nar/gkt765
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- Article
Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study.
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- Nucleic Acids Research, 2010, v. 38, n. 9, p. 2975, doi. 10.1093/nar/gkp1230
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- Article
UEP: an open-source and fast classifier for predicting the impact of mutations in protein–protein complexes.
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- Bioinformatics, 2021, v. 37, n. 3, p. 334, doi. 10.1093/bioinformatics/btaa708
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- Article
Diverging co-translational protein complex assembly pathways are governed by interface energy distribution.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46881-w
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Computer applications for prediction of protein-protein interactions and rational drug design.
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- Advances & Applications in Bioinformatics & Chemistry, 2009, v. 2, p. 101
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- Article
LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains.
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- PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021614
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- Article
Inferring the microscopic surface energy of protein-protein interfaces from mutation data.
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- Proteins, 2015, v. 83, n. 4, p. 640, doi. 10.1002/prot.24761
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Blind prediction of interfacial water positions in CAPRI.
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- Proteins, 2014, v. 82, n. 4, p. 620, doi. 10.1002/prot.24439
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Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges.
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- Proteins, 2013, v. 81, n. 12, p. 2192, doi. 10.1002/prot.24387
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- Article
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
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- Proteins, 2013, v. 81, n. 11, p. 1980, doi. 10.1002/prot.24356
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A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data.
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- Proteins, 2012, v. 80, n. 7, p. 1872, doi. 10.1002/prot.24075
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The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona.
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- Proteins, 2010, v. 78, n. 15, p. 3065, doi. 10.1002/prot.22801
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Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.
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- Proteins, 2010, v. 78, n. 15, p. 3182, doi. 10.1002/prot.22773
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Present and future challenges and limitations in protein-protein docking.
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- Proteins, 2010, v. 78, n. 1, p. 95, doi. 10.1002/prot.22564
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Optimal protein-RNA area, OPRA: A propensity-based method to identify RNA-binding sites on proteins.
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- Proteins, 2010, v. 78, n. 1, p. 25, doi. 10.1002/prot.22527
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- Article
Docking analysis of transient complexes: Interaction of ferredoxin-NADP<sup>+</sup> reductase with ferredoxin and flavodoxin.
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- Proteins, 2008, v. 72, n. 3, p. 848, doi. 10.1002/prot.21979
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- Article
Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins.
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- Proteins, 2008, v. 70, n. 1, p. 294, doi. 10.1002/prot.21610
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Prediction and scoring of docking poses with pyDock.
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- Proteins, 2007, v. 69, n. 4, p. 852, doi. 10.1002/prot.21796
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pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.
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- Proteins, 2007, v. 68, n. 2, p. 503, doi. 10.1002/prot.21419
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Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.
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- Proteins, 2007, v. 68, n. 1, p. 131, doi. 10.1002/prot.21390
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Improving CAPRI predictions: Optimized desolvation for rigid-body docking.
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- Proteins, 2005, v. 60, n. 2, p. 308, doi. 10.1002/prot.20575
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Optimal docking area: A new method for predicting protein-protein interaction sites.
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- Proteins, 2005, v. 58, n. 1, p. 134, doi. 10.1002/prot.20285
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ICM-DISCO docking by global energy optimization with fully flexible side-chains.
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- Proteins, 2003, v. 52, n. 1, p. 113
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L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09837-z
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- Article
The scoring of poses in protein-protein docking: current capabilities and future directions.
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- BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-286
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- Article
Protein docking by Rotation-Based UniformSampling (RotBUS) with fast computing ofintermolecular contact distance and residuedesolvation.
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- BMC Bioinformatics, 2010, v. 11, p. 352, doi. 10.1186/1471-2105-11-352
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In silico docking of urokinase plasminogen activator and integrins.
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- BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S2-S8
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Cell biology: Brief encounters bolster contacts.
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- Nature, 2006, v. 444, n. 7117, p. 279, doi. 10.1038/nature05306
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Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization.
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- PLoS Computational Biology, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003216
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- Article
Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments.
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- PLoS Computational Biology, 2009, v. 5, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000490
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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study.
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- Proteomics, 2023, v. 23, n. 17, p. 1, doi. 10.1002/pmic.202200323
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- Article
New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes.
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- Plant & Cell Physiology, 2021, v. 62, n. 7, p. 1082, doi. 10.1093/pcp/pcab044
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Structural Basis for Rab1 De-AMPylation by the <i>Legionella pneumophila</i> Effector SidD
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- PLoS Pathogens, 2013, v. 9, n. 5, p. 1, doi. 10.1371/journal.ppat.1003382
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Structural bases for the higher adherence to ACE2 conferred by the SARS‐CoV‐2 spike Q498Y substitution.
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- Acta Crystallographica: Section D, Structural Biology, 2022, v. 78, n. 9, p. 1156, doi. 10.1107/S2059798322007677
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- Article
Structural basis for the dominant or recessive character of GLIALCAM mutations found in leukodystrophies.
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- Human Molecular Genetics, 2020, v. 29, n. 7, p. 1107, doi. 10.1093/hmg/ddaa009
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- Article
Prediction of protein binding sites and hot spots.
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- WIREs: Computational Molecular Science, 2011, v. 1, n. 5, p. 680, doi. 10.1002/wcms.45
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- Article
Dissection and prediction of RNA-binding sites on proteins.
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- Biomolecular Concepts, 2010, v. 1, n. 5/6, p. 345, doi. 10.1515/BMC.2010.037
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- Article
multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities.
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- Nucleic Acids Research, 2022, v. 50, n. 22, p. 13063, doi. 10.1093/nar/gkac1119
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- Article
Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases.
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- Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-30202-5
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- Article
A model of a transmembrane drug-efflux pump from Gram-negative bacteria
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- FEBS Letters, 2004, v. 578, n. 1/2, p. 5, doi. 10.1016/j.febslet.2004.10.097
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- Article
Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering.
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- Protein Science: A Publication of the Protein Society, 2009, v. 18, n. 4, p. 716, doi. 10.1002/pro.83
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Soft protein-protein docking in internal coordinates.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 2, p. 280, doi. 10.1110/ps.19202
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Integrative modeling of protein‐protein interactions with pyDock for the new docking challenges.
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- Proteins, 2020, v. 88, n. 8, p. 999, doi. 10.1002/prot.25858
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- Article
A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.
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- Proteins, 2017, v. 85, n. 7, p. 1287, doi. 10.1002/prot.25289
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pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions.
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- Proteins, 2017, v. 85, n. 3, p. 487, doi. 10.1002/prot.25184
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- Article