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A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51933-2
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Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
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- Angewandte Chemie, 2016, v. 128, n. 19, p. 5797, doi. 10.1002/ange.201511351
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- Article
ARTS: alignment of RNA tertiary structures.
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- Bioinformatics, 2005, v. 21, p. ii47, doi. 10.1093/bioinformatics/bti1108
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- Article
Activation mechanisms of clinically distinct B‐Raf V600E and V600K mutants.
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- Cancer Communications, 2023, v. 43, n. 3, p. 405, doi. 10.1002/cac2.12395
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- Article
The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway.
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- Scientific Reports, 2015, p. 13128, doi. 10.1038/srep13128
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Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways.
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- British Journal of Pharmacology, 2012, v. 165, n. 7, p. 2110, doi. 10.1111/j.1476-5381.2011.01793.x
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- Article
Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios.
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- Journal of Molecular Recognition, 2010, v. 23, n. 2, p. 232, doi. 10.1002/jmr.990
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- Article
Visualizing RNA conformational and architectural heterogeneity in solution.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-36184-x
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Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network-Based Drug Design.
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- Molecular Informatics, 2014, v. 33, n. 6/7, p. 463, doi. 10.1002/minf.201400029
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Activation of orphan receptor GPR132 induces cell differentiation in acute myeloid leukemia.
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- Cell Death & Disease, 2022, v. 13, n. 11, p. 1, doi. 10.1038/s41419-022-05434-z
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The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops
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- FEBS Letters, 2012, v. 586, n. 13, p. 1795, doi. 10.1016/j.febslet.2012.05.016
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Structural similarity of genetically interacting proteins.
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- BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-69
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Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains.
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- PEDS: Protein Engineering, Design & Selection, 2017, v. 30, n. 1, p. 67, doi. 10.1093/protein/gzw065
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- Article
Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization.
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- PEDS: Protein Engineering, Design & Selection, 2016, v. 29, n. 9, p. 347, doi. 10.1093/protein/gzw033
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Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways.
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- PEDS: Protein Engineering, Design & Selection, 2005, v. 18, n. 1, p. 11, doi. 10.1093/protein/gzh095
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- Article
Disruption of Ca<sup>2+</sup>/calmodulin:KSR1 interaction lowers ERK activation.
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- Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 5, p. 1, doi. 10.1002/pro.4982
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- Article
Higher‐order interactions of Bcr‐Abl can broaden chronic myeloid leukemia (CML) drug repertoire.
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- Protein Science: A Publication of the Protein Society, 2023, v. 32, n. 1, p. 1, doi. 10.1002/pro.4504
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Multiple-Targeting and Conformational Selection in the Estrogen Receptor: Computation and Experiment.
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- Chemical Biology & Drug Design, 2011, v. 78, n. 1, p. 137, doi. 10.1111/j.1747-0285.2011.01119.x
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- Article
Data‐driven model of the KRas4B/Calmodulin complex.
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- FASEB Journal, 2021, v. 35, p. N.PAG, doi. 10.1096/fasebj.2021.35.S1.04058
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- Article
Autoinhibition can identify rare driver mutations and advise pharmacology.
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- FASEB Journal, 2020, v. 34, n. 1, p. 16, doi. 10.1096/fj.201901341R
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Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA.
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- FASEB Journal, 2019, v. 33, n. 3, p. 4225, doi. 10.1096/fj.201801973R
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- Article
The higher level of complexity of K-Ras4B activation at the membrane.
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- FASEB Journal, 2016, v. 30, n. 4, p. 1643, doi. 10.1096/fj.15-279091
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- Article
Comparing interfacial dynamics in protein-proteincomplexes: an elastic network approach.
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- BMC Structural Biology, 2010, v. 10, p. 26, doi. 10.1186/1472-6807-10-26
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The structural network of Interleukin-10 and its implications in inflammation and cancer.
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- BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S4-S2
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- Article
Mechanism of activation and the rewired network: New drug design concepts.
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- Medicinal Research Reviews, 2022, v. 42, n. 2, p. 770, doi. 10.1002/med.21863
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- Article
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing.
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- Medicinal Research Reviews, 2020, v. 40, n. 6, p. 2386, doi. 10.1002/med.21709
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- Article
Computational Structural Biology: Successes, Future Directions, and Challenges.
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- Molecules, 2019, v. 24, n. 3, p. 637, doi. 10.3390/molecules24030637
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Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid-β Aggregation.
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- Israel Journal of Chemistry, 2017, v. 57, n. 7/8, p. 622, doi. 10.1002/ijch.201600093
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- Article
My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02269-3
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- Article
My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02269-3
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- Article
Bioinformatics Study of Cancer-Related Mutations within p53 Phosphorylation Site Motifs.
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- International Journal of Molecular Sciences, 2014, v. 15, n. 8, p. 13275, doi. 10.3390/ijms150813275
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- Article
A formal MIM specification and tools for the common exchange of MIM diagrams: an XMLBased format, an API, and a validation method.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 167, doi. 10.1186/1471-2105-12-167
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- Article
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing.
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- Journal of Computer-Aided Molecular Design, 2013, v. 27, n. 1, p. 31, doi. 10.1007/s10822-012-9623-5
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- Article
Shape complementarity at protein-protein interfaces.
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- Biopolymers, 1994, v. 34, n. 7, p. 933, doi. 10.1002/bip.360340711
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- Article
A new precision medicine initiative at the dawn of exascale computing.
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- Signal Transduction & Targeted Therapy, 2021, v. 6, n. 1, p. 1, doi. 10.1038/s41392-020-00420-3
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- Article
Reprogramming immunosuppressive myeloid cells facilitates immunotherapy for colorectal cancer.
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- EMBO Molecular Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.15252/emmm.202012798
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- Article
Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
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- Angewandte Chemie International Edition, 2016, v. 55, n. 19, p. 5703, doi. 10.1002/anie.201511351
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- Article
Single Mutations in Tau Modulate the Populations of Fibril Conformers through Seed Selection.
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- Angewandte Chemie International Edition, 2014, v. 53, n. 6, p. 1590, doi. 10.1002/anie.201308473
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- Article
Association of putative concave protein-binding sites with the fluctuation behavior of residues.
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- Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 10, p. 2265, doi. 10.1110/ps.051815006
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Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families.
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- Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 9, p. 2120, doi. 10.1110/ps.062249106
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- Article
The implications of higher (or lower) success in secondary structure prediction of chain fragments.
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- Protein Science: A Publication of the Protein Society, 2005, v. 14, n. 8, p. 1943, doi. 10.1110/ps.051581805
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- Article
In silico protein design by combinatorial assembly of protein building blocks.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 10, p. 2753, doi. 10.1110/ps.04774004
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- Article
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 4, p. 1043, doi. 10.1110/ps.03484604
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Multiple structural alignment by secondary structures: Algorithm and applications.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 11, p. 2492, doi. 10.1110/ps.03200603
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Energy landscape and dynamics of the β-hairpin G peptide and its isomers: Topology and sequences.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 9, p. 1882, doi. 10.1110/ps.0306103
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- Article
SiteLight: Binding-site prediction using phage display libraries.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 7, p. 1344, doi. 10.1110/ps.0237103
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- Article
Reducing the computational complexity of protein folding via fragment folding and assembly.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 6, p. 1177, doi. 10.1110/ps.0232903
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- Article
Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 10, p. 2335, doi. 10.1110/ps.4270102
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Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 7, p. 1753, doi. 10.1110/ps.4100102
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- Article
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 2, p. 184, doi. 10.1110/ps.21302
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- Article