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Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation.
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- Cell Biochemistry & Biophysics, 2013, v. 67, n. 3, p. 1193, doi. 10.1007/s12013-013-9638-0
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SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
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- Bioinformatics, 2005, v. 21, n. 18, p. 3615, doi. 10.1093/bioinformatics/bti582
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- Article
Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.
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- Scientific Reports, 2015, p. 11476, doi. 10.1038/srep11476
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- Article
GJB3 promotes pancreatic cancer liver metastasis by enhancing the polarization and survival of neutrophil.
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- Frontiers in Immunology, 2022, v. 13, p. 1, doi. 10.3389/fimmu.2022.983116
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- Article
DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels.
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- Genome Biology, 2013, v. 14, n. 3, p. 1, doi. 10.1186/gb-2013-14-3-r23
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- Article
Soft-sediment deformation structures induced by rapid sedimentation in Early Cretaceous turbidites, Lingshan Island, eastern China.
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- Canadian Journal of Earth Sciences, 2018, v. 55, n. 2, p. 118, doi. 10.1139/cjes-2017-0106
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- Article
DNA sequence repeats identify numerous Type I restriction‐modification systems that are potential epigenetic regulators controlling phase‐variable regulons; phasevarions.
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- FASEB Journal, 2020, v. 34, n. 1, p. 1038, doi. 10.1096/fj.201901536RR
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Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides.
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- FASEB Journal, 2019, v. 33, n. 2, p. 2095, doi. 10.1096/fj.201700613RR
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SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network.
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- PLoS Computational Biology, 2023, v. 19, n. 12, p. 1, doi. 10.1371/journal.pcbi.1011330
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YesU from Bacillus subtilis preferentially binds fucosylated glycans.
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- Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-31241-8
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- Article
From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs.
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- Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.650926
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Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation.
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- Human Molecular Genetics, 2014, v. 23, n. 11, p. 3024, doi. 10.1093/hmg/ddu019
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Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes.
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- Human Molecular Genetics, 2006, v. 15, n. 8, p. 1313, doi. 10.1093/hmg/ddl051
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- Article
Multiple sequence alignment-based RNA language model and its application to structural inference.
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- Nucleic Acids Research, 2024, v. 52, n. 1, p. e3, doi. 10.1093/nar/gkad1031
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EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments.
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- Nucleic Acids Research, 2024, v. 52, n. D1, p. D98, doi. 10.1093/nar/gkad1057
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- Article
Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor.
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- Nature Communications, 2017, v. 8, n. 3, p. 14902, doi. 10.1038/ncomms14902
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- Article
RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants.
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- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1847-4
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- Article
Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers.
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- International Journal of Molecular Sciences, 2018, v. 19, n. 4, p. 1186, doi. 10.3390/ijms19041186
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Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.
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- International Journal of Molecular Sciences, 2018, v. 19, n. 3, p. 885, doi. 10.3390/ijms19030885
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- Article
In-silico prediction of disorder content using hybrid sequence representation.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 245, doi. 10.1186/1471-2105-12-245
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- Article
Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory.
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- Biopolymers, 1996, v. 38, n. 2, p. 273, doi. 10.1002/(SICI)1097-0282(199602)38:2<273::AID-BIP11>3.0.CO;2-G
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3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next?
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- National Science Review, 2023, v. 10, n. 12, p. 1, doi. 10.1093/nsr/nwad259
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Disulfiram inhibits liver fibrosis in rats by suppressing hepatic stellate cell activation and viability.
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- BMC Pharmacology & Toxicology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s40360-022-00583-5
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Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
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- Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baz138
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Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
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- Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz085
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- Article
Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana.
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- Protein Science: A Publication of the Protein Society, 2012, v. 21, n. 6, p. 828, doi. 10.1002/pro.2066
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- Article
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions.
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- Protein Science: A Publication of the Protein Society, 2008, v. 17, n. 7, p. 1212, doi. 10.1110/ps.033480.107
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DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile.
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- Protein Science: A Publication of the Protein Society, 2007, v. 16, n. 5, p. 947, doi. 10.1110/ps.062597307
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- Article
Protein flexibility prediction by an all-atom mean-field statistical theory.
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- Protein Science: A Publication of the Protein Society, 2005, v. 14, n. 7, p. 1772, doi. 10.1110/ps.041311005
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Critical nucleation size in the folding of small apparently two-state proteins.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 5, p. 1173, doi. 10.1110/ps.03587604
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An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 2, p. 400, doi. 10.1110/ps.03348304
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- Article
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 2, p. 391, doi. 10.1110/ps.03411904
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Thermodynamics and stability of a β-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models.
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- Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 1, p. 40, doi. 10.1110/ps.03162804
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CORRECTION.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 9, p. 2121, doi. 10.1002/pro.122121
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Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method.
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- Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 7, p. 1547, doi. 10.1110/ps.0305103
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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 11, p. 2714, doi. 10.1110/ps.0217002
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The dual role of a loop with low loop contact distance in folding and domain swapping.
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- Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 7, p. 1695, doi. 10.1110/ps.0205002
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The calorimetric criterion for a two-state process revisited.
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- Protein Science: A Publication of the Protein Society, 1999, v. 8, n. 5, p. 1064
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DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins.
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- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1620-1
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- Article
FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION.
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- Journal of Bioinformatics & Computational Biology, 2005, v. 3, n. 5, p. 1151, doi. 10.1142/S0219720005001430
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- Article
Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening.
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- Applied Microbiology & Biotechnology, 2016, v. 100, n. 20, p. 8745, doi. 10.1007/s00253-016-7615-4
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- Article
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model.
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- Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad173
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EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac583
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Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
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- Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac112
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Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
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- Briefings in Bioinformatics, 2018, v. 19, n. 3, p. 482, doi. 10.1093/bib/bbw129
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- Article
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.
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- Bioinformatics, 2022, v. 38, n. 16, p. 3900, doi. 10.1093/bioinformatics/btac421
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- Article
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.
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- Bioinformatics, 2022, v. 38, n. 7, p. 1888, doi. 10.1093/bioinformatics/btac053
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- Article
Structure-aware protein–protein interaction site prediction using deep graph convolutional network.
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- Bioinformatics, 2022, v. 38, n. 1, p. 125, doi. 10.1093/bioinformatics/btab643
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- Article
De novo protein design by an energy function based on series expansion in distance and orientation dependence.
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- Bioinformatics, 2022, v. 38, n. 1, p. 86, doi. 10.1093/bioinformatics/btab598
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RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.
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- Bioinformatics, 2021, v. 37, n. 20, p. 3494, doi. 10.1093/bioinformatics/btab391
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- Article