RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.
Bioinform., September, 2023
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.
Briefings Bioinform., July, 2023
NACDDB: Nucleic Acid Circular Dichroism Database.
Nucleic Acids Res., January, 2023
fingeRNAt - A novel tool for high-throughput analysis of nucleic acid-ligand interactions.
PLoS Comput. Biol., 2022
DNAzymeBuilder, a web application for <i>in situ</i> generation of RNA/DNA-cleaving deoxyribozymes.
Nucleic Acids Res., 2022
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.
PLoS Comput. Biol., 2021
DNAmoreDB, a database of DNAzymes.
Nucleic Acids Res., 2021
RNAProbe: a web server for normalization and analysis of RNA structure probing data.
Nucleic Acids Res., 2020
RNA 3D structure prediction guided by independent folding of homologous sequences.
BMC Bioinform., 2019
RRMdb - an evolutionary-oriented database of RNA recognition motif sequences.
Database J. Biol. Databases Curation, 2019
MODOMICS: a database of RNA modification pathways. 2017 update.
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Nucleic Acids Res., 2018
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
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Nucleic Acids Res., 2018
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.
Nucleic Acids Res., 2016
NPDock: a web server for protein-nucleic acid docking.
Nucleic Acids Res., 2015
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
BMC Bioinform., 2015
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
Bioinform., 2015
RNA Bricks - a database of RNA 3D motifs and their interactions.
Nucleic Acids Res., 2014
Bioinformatics and Computational Biology in Poland.
PLoS Comput. Biol., 2013
QA-RecombineIt: a server for quality assessment and recombination of protein models.
Nucleic Acids Res., 2013
RNApathwaysDB - a database of RNA maturation and decay pathways.
Nucleic Acids Res., 2013
MODOMICS: a database of RNA modification pathways - 2013 update.
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Nucleic Acids Res., 2013
Intrinsic Disorder in the Human Spliceosomal Proteome.
PLoS Comput. Biol., 2012
RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.
BMC Bioinform., 2012
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement.
BMC Bioinform., 2012
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins.
BMC Bioinform., 2012
Molecular evolution of dihydrouridine synthases.
BMC Bioinform., 2012
MetalionRNA: computational predictor of metal-binding sites in RNA structures.
Bioinform., 2012
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes.
Bioinform., 2012
A toolbox for developing bioinformatics software.
Briefings Bioinform., 2012
REPAIRtoire - a database of DNA repair pathways.
Nucleic Acids Res., 2011
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking.
BMC Bioinform., 2011
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinform., 2011
RNA tertiary structure prediction with ModeRNA.
Briefings Bioinform., 2011
ModeRNA builds RNA 3D Models from Template Structures.
ERCIM News, 2010
FILTREST3D: discrimination of structural models using restraints from experimental data.
Bioinform., 2010
MODOMICS: a database of RNA modification pathways, update 2008
Nucleic Acids Res., 2009
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors.
Algorithms, 2009
MetaMQAP: A meta-server for the quality assessment of protein models.
BMC Bioinform., 2008
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
BMC Bioinform., 2007
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.
Bioinform., 2007
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
Bioinform., 2007
MODOMICS: a database of RNA modification pathways.
Nucleic Acids Res., 2006
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
BMC Bioinform., 2005
DNase II is a member of the phospholipase D superfamily.
Bioinform., 2005
COLORADO3D, a web server for the visual analysis of protein structures.
Nucleic Acids Res., 2004
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination.
Proceedings of the Biocomputing 2004, 2004
GeneSilico protein structure prediction meta-server.
Nucleic Acids Res., 2003
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure.
Nucleic Acids Res., 2003
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of <i>S</i>-adenosylmethionine to three crystal structures.
BMC Bioinform., 2003
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003
RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
BMC Bioinform., 2002
Fold-recognition detects an error in the Protein Data Bank.
Bioinform., 2002
mRNA: guanine-<i>N</i>7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
BMC Bioinform., 2001
Structure prediction meta server.
Bioinform., 2001
Comparison of protein structures reveals monophyletic origin of AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
Silico Biol., 1999