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Multi-task learning to leverage partially annotated data for PPI interface prediction.
- Published in:
- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-13951-2
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- Article
Towards a knowledge graph for pre-/probiotics and microbiota–gut–brain axis diseases.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-21735-x
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- Article
ProteinGLUE multi-task benchmark suite for self-supervised protein modeling.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-19608-4
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- Article
Multi-Harmony: detecting functional specificity from sequence alignment.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W35, doi. 10.1093/nar/gkq415
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- Article
Sequence harmony: detecting functional specificity from alignments.
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- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W495, doi. 10.1093/nar/gkm406
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- Article
Sequence comparison by sequence harmony identifies subtype-specific functional sites.
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- Nucleic Acids Research, 2006, v. 34, n. 22, p. 6540, doi. 10.1093/nar/gkl901
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- Article
In vitro evolution of styrene monooxygenase from Pseudomonas putida CA-3 for improved epoxide synthesis.
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- Applied Microbiology & Biotechnology, 2010, v. 85, n. 4, p. 995, doi. 10.1007/s00253-009-2096-3
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- Article
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.
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- Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad771
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- Article
PIPENN: protein interface prediction from sequence with an ensemble of neural nets.
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- Bioinformatics, 2022, v. 38, n. 8, p. 2111, doi. 10.1093/bioinformatics/btac071
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- Article
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes.
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- Bioinformatics, 2021, v. 37, n. 20, p. 3421, doi. 10.1093/bioinformatics/btab321
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- Article
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.
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- Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 589, doi. 10.1093/bib/bbt023
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- Article
HIV-1 Replication Fitness of HLA-B*57/58:01 CTL Escape Variants Is Restored by the Accumulation of Compensatory Mutations in Gag.
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- PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0081235
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- Article
On defining the dynamics of hydrophobic patches on protein surfaces.
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- Proteins, 2008, v. 72, n. 1, p. 105, doi. 10.1002/prot.21924
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- Article
Online biophysical predictions for SARS-CoV-2 proteins.
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- BMC Molecular & Cell Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12860-021-00362-w
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- Article
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case.
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- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0758-y
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- Article
Structure and function analysis of flexible alignment regions in proteins.
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- BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S13-P6
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- Publication type:
- Article
Ten quick tips for sequence-based prediction of protein properties using machine learning.
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- PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010669
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- Article
Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling.
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- PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0155743
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- Article
CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.
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- PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0155251
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- Article
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.
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- Journal of Biomolecular NMR, 2002, v. 23, n. 3, p. 181, doi. 10.1023/A:1019854626147
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- Article
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.
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- Bioinformatics, 2008, v. 24, n. 4, p. 492, doi. 10.1093/bioinformatics/btm636
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- Article
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
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- Bioinformatics, 2008, v. 24, n. 1, p. 18, doi. 10.1093/bioinformatics/btm537
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- Publication type:
- Article
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems.
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- Journal of Computational Chemistry, 1999, v. 20, n. 8, p. 786, doi. 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B
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- Article
Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.
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- Protein Science: A Publication of the Protein Society, 2007, v. 16, n. 3, p. 420, doi. 10.1110/ps.062224407
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- Article
The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern.
- Published in:
- PLoS Computational Biology, 2019, v. 15, n. 5, p. 1, doi. 10.1371/journal.pcbi.1007061
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- Article
A framework for exhaustive modelling of genetic interaction patterns using Petri nets.
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- Bioinformatics, 2020, v. 36, n. 7, p. 2142, doi. 10.1093/bioinformatics/btz917
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- Article
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.
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- Bioinformatics, 2019, v. 35, n. 24, p. 5315, doi. 10.1093/bioinformatics/btz572
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- Article
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.
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- Bioinformatics, 2019, v. 35, n. 22, p. 4794, doi. 10.1093/bioinformatics/btz428
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- Article
Training for translation between disciplines: a philosophy for life and data sciences curricula.
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- Bioinformatics, 2018, v. 34, n. 13, p. i4, doi. 10.1093/bioinformatics/bty233
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- Article
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.
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- Bioinformatics, 2017, v. 33, n. 10, p. 1479, doi. 10.1093/bioinformatics/btx005
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- Article
BioASF: a framework for automatically generating executable pathway models specified in BioPAX.
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- Bioinformatics, 2016, v. 32, n. 12, p. i60, doi. 10.1093/bioinformatics/btw250
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- Article
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.
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- Bioinformatics, 2014, v. 30, n. 3, p. 326, doi. 10.1093/bioinformatics/btt675
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- Article
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.
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- Bioinformatics, 2013, v. 29, n. 13, p. i80, doi. 10.1093/bioinformatics/btt243
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- Article
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development.
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- 2009
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- Correction Notice
Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS Through the GromPy Python Interface Module.
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- Journal of Computational Chemistry, 2012, v. 33, n. 12, p. 1207, doi. 10.1002/jcc.22947
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- Article
HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity.
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- Retrovirology, 2013, v. 10, n. 1, p. 1, doi. 10.1186/1742-4690-10-102
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- Article
Motif-Aware PRALINE: Improving the alignment of motif regions.
- Published in:
- PLoS Computational Biology, 2018, v. 14, n. 11, p. 1, doi. 10.1371/journal.pcbi.1006547
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- Article