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Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server.
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- Proteins, 2023, v. 91, n. 12, p. 1822, doi. 10.1002/prot.26587
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The ClusPro AbEMap web server for the prediction of antibody epitopes.
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- Nature Protocols, 2023, v. 18, n. 6, p. 1814, doi. 10.1038/s41596-023-00826-7
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Mapping of antibody epitopes based on docking and homology modeling.
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- Proteins, 2023, v. 91, n. 2, p. 171, doi. 10.1002/prot.26420
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Novel p.G250A Mutation Associated with Chronic Pancreatitis Highlights Misfolding-Prone Region in Carboxypeptidase A1 (CPA1).
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- International Journal of Molecular Sciences, 2022, v. 23, n. 24, p. 15463, doi. 10.3390/ijms232415463
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Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap.
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- Acta Crystallographica: Section D, Structural Biology, 2022, v. 78, n. 6, p. 690, doi. 10.1107/S2059798322002741
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Assessing the binding properties of CASP14 targets and models.
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- Proteins, 2021, v. 89, n. 12, p. 1922, doi. 10.1002/prot.26209
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Exploring protein hotspots by optimized fragment pharmacophores.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23443-y
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Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45.
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- Proteins, 2020, v. 88, n. 8, p. 1037, doi. 10.1002/prot.25871
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ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking.
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- Proteins, 2020, v. 88, n. 8, p. 1082, doi. 10.1002/prot.25887
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Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking.
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- Proteins, 2019, v. 87, n. 12, p. 1241, doi. 10.1002/prot.25808
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New additions to the Clus Pro server motivated by CAPRI.
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- Proteins, 2017, v. 85, n. 3, p. 435, doi. 10.1002/prot.25219
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The ClusPro web server for protein–protein docking.
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- Nature Protocols, 2017, v. 12, n. 2, p. 255, doi. 10.1038/nprot.2016.169
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A benchmark testing ground for integrating homology modeling and protein docking.
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- Proteins, 2017, v. 85, n. 1, p. 10, doi. 10.1002/prot.25063
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Accounting for pairwise distance restraints in FFT-based protein--protein docking.
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- Bioinformatics, 2016, v. 32, n. 21, p. 3342, doi. 10.1093/bioinformatics/btw306
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Focused grid-based resampling for protein docking and mapping.
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- Journal of Computational Chemistry, 2016, v. 37, n. 11, p. 961, doi. 10.1002/jcc.24273
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Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro.
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- Journal of Computational Chemistry, 2015, v. 36, n. 20, p. 1568, doi. 10.1002/jcc.23952
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The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
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- Nature Protocols, 2015, v. 10, n. 5, p. 733, doi. 10.1038/nprot.2015.043
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- Article
Ligand Binding and Activation of PPARγ by Firemaster® 550: Effects on Adipogenesis and Osteogenesis in Vitro.
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- Environmental Health Perspectives, 2014, v. 122, n. 11, p. 1225, doi. 10.1289/ehp.1408111
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Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces.
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- PLoS Computational Biology, 2014, v. 10, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003872
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- Article
How proteins bind macrocycles.
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- Nature Chemical Biology, 2014, v. 10, n. 9, p. 723, doi. 10.1038/nchembio.1584
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How good is automated protein docking?
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- Proteins, 2013, v. 81, n. 12, p. 2159, doi. 10.1002/prot.24403
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Sampling and scoring: A marriage made in heaven.
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- Proteins, 2013, v. 81, n. 11, p. 1874, doi. 10.1002/prot.24343
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FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
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- Bioinformatics, 2013, v. 29, n. 9, p. 1218, doi. 10.1093/bioinformatics/btt102
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Application of asymmetric statistical potentials to antibody–protein docking.
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- Bioinformatics, 2012, v. 28, n. 20, p. 2608, doi. 10.1093/bioinformatics/bts493
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- Article
Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.
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- Nucleic Acids Research, 2012, v. 40, n. 16, p. 7644, doi. 10.1093/nar/gks519
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- Article
FTMAP: extended protein mapping with user-selected probe molecules.
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- Nucleic Acids Research, 2012, v. 40, p. W271, doi. 10.1093/nar/gks441
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- Article
A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy.
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- PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0040234
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Minimal ensembles of side chain conformers for modeling protein-protein interactions.
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- Proteins, 2012, v. 80, n. 2, p. 591, doi. 10.1002/prot.23222
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- Article
FTSite: high accuracy detection of ligand binding sites on unbound protein structures.
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- Bioinformatics, 2012, v. 28, n. 2, p. 286, doi. 10.1093/bioinformatics/btr651
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Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.
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- Proteins, 2010, v. 78, n. 15, p. 3124, doi. 10.1002/prot.22835
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- Article
Domain motion and interdomain hot spots in a multidomain enzyme.
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- Protein Science: A Publication of the Protein Society, 2010, v. 19, n. 9, p. 1662, doi. 10.1002/pro.446
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Structural insights into recognition of β2-glycoprotein I by the lipoprotein receptors.
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- Proteins, 2009, v. 77, n. 4, p. 940, doi. 10.1002/prot.22519
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Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.
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- Journal of Computer-Aided Molecular Design, 2009, v. 23, n. 8, p. 491, doi. 10.1007/s10822-009-9283-2
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- Article
Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques.
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- Bioinformatics, 2009, v. 25, n. 5, p. 621, doi. 10.1093/bioinformatics/btp036
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- Article
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions.
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- Bioinformatics, 2008, v. 24, n. 17, p. 1865, doi. 10.1093/bioinformatics/btn334
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- Article
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.
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- Proteins, 2008, v. 72, n. 3, p. 993, doi. 10.1002/prot.21997
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- Article
Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble.
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- Chemical Biology & Drug Design, 2008, v. 71, n. 2, p. 106, doi. 10.1111/j.1747-0285.2007.00614.x
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Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.
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- Proteins, 2007, v. 69, n. 4, p. 734, doi. 10.1002/prot.21754
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ClusPro: Performance in CAPRI rounds 6-11 and the new server.
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- Proteins, 2007, v. 69, n. 4, p. 781, doi. 10.1002/prot.21795
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PIPER: An FFT-based protein docking program with pairwise potentials.
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- Proteins, 2006, v. 65, n. 2, p. 392, doi. 10.1002/prot.21117
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Classification of protein complexes based on docking difficulty.
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- Proteins, 2005, v. 60, n. 2, p. 176, doi. 10.1002/prot.20554
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Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
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- Proteins, 2005, v. 60, n. 2, p. 239, doi. 10.1002/prot.20564
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PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d206
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Consensus alignment server for reliable comparative modeling with distant templates.
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- Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w50, doi. 10.1093/nar/gkh456
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ClusPro: a fully automated algorithm for protein–protein docking.
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- Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w96, doi. 10.1093/nar/gkh354
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- Article
ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
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- Bioinformatics, 2004, v. 20, n. 1, p. 45, doi. 10.1093/bioinformatics/btg371
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- Article
Combination of scoring functions improves discrimination in proteinprotein docking.
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- Proteins, 2003, v. 53, n. 4, p. 840, doi. 10.1002/prot.10473
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CAPRI: A Critical Assessment of PRedicted Interactions.
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- Proteins, 2003, v. 52, n. 1, p. 2, doi. 10.1002/prot.10381
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Algorithms for computational solvent mapping of proteins.
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- Proteins, 2003, v. 51, n. 3, p. 340, doi. 10.1002/prot.10287
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Improved mapping of protein binding sites.
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- Journal of Computer-Aided Molecular Design, 2003, v. 17, n. 2-4, p. 173, doi. 10.1023/A:1025369923311
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- Article