Published in BMC Bioinformatics on June 16, 2010
WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res (2011) 1.13
RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures. Nucleic Acids Res (2011) 1.01
Detecting and comparing non-coding RNAs in the high-throughput era. Int J Mol Sci (2013) 0.78
COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. Nucleic Acids Res (2014) 0.77
MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics (2015) 0.76
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science (2000) 28.25
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol (2007) 2.81
SCOR: a Structural Classification of RNA database. Nucleic Acids Res (2002) 2.79
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res (2003) 2.42
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol Cell (2008) 2.37
Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. Nucleic Acids Res (2003) 2.10
Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci U S A (2002) 2.03
Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci U S A (2004) 2.03
RNA structural motifs: building blocks of a modular biomolecule. Q Rev Biophys (2006) 1.88
The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Res (2004) 1.70
ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67
RNA structure: the long and the short of it. Curr Opin Struct Biol (2005) 1.63
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res (2007) 1.57
Representation, searching and discovery of patterns of bases in complex RNA structures. J Comput Aided Mol Des (2003) 1.27
Species-specific antibiotic-ribosome interactions: implications for drug development. Biol Chem (2005) 1.27
SARA: a server for function annotation of RNA structures. Nucleic Acids Res (2009) 1.25
Analysis and classification of RNA tertiary structures. RNA (2008) 1.20
Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins (1999) 1.16
SARSA: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res (2008) 1.14
Finding 3D motifs in ribosomal RNA structures. Nucleic Acids Res (2009) 1.01
QMEAN: A comprehensive scoring function for model quality assessment. Proteins (2008) 3.90
The PASTA server for protein aggregation prediction. Protein Eng Des Sel (2007) 1.76
ESpritz: accurate and fast prediction of protein disorder. Bioinformatics (2011) 1.67
LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy. Hum Mutat (2009) 1.58
A Mek1-Mek2 heterodimer determines the strength and duration of the Erk signal. Nat Struct Mol Biol (2009) 1.48
Increased hydrophobicity at the N terminus/membrane interface impairs gating of the severe combined immunodeficiency-related ORAI1 mutant. J Biol Chem (2009) 1.39
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res (2006) 1.37
MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics (2012) 1.36
CX, an algorithm that identifies protruding atoms in proteins. Bioinformatics (2002) 1.33
DPX: for the analysis of the protein core. Bioinformatics (2003) 1.29
RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics (2011) 1.25
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins (2009) 1.24
Atom depth as a descriptor of the protein interior. Biophys J (2003) 1.24
Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22
Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily. Antioxid Redox Signal (2008) 1.15
Unique features of the sodC-encoded superoxide dismutase from Mycobacterium tuberculosis, a fully functional copper-containing enzyme lacking zinc in the active site. J Biol Chem (2004) 1.15
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations. Proteins (2004) 1.13
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Res (2011) 1.10
Structural insights into the function of human caveolin 1. Biochem Biophys Res Commun (2005) 1.10
Atom depth in protein structure and function. Trends Biochem Sci (2003) 1.09
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform. Bioinformatics (2009) 1.02
From autoinhibition to inhibition in trans: the Raf-1 regulatory domain inhibits Rok-alpha kinase activity. J Cell Biol (2009) 1.01
The thioredoxin specificity of Drosophila GPx: a paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases. J Mol Biol (2006) 1.00
Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng (2003) 1.00
RepeatsDB: a database of tandem repeat protein structures. Nucleic Acids Res (2013) 0.97
Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer. J Mol Biol (2007) 0.96
NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation. BMC Genomics (2014) 0.94
Targeted proteolysis of plectin isoform 1a accounts for hemidesmosome dysfunction in mice mimicking the dominant skin blistering disease EBS-Ogna. PLoS Genet (2011) 0.93
The SSEA server for protein secondary structure alignment. Bioinformatics (2004) 0.93
Consensus prediction of protein conformational disorder from amino acidic sequence. Open Biochem J (2008) 0.93
Low density lipoprotein misfolding and amyloidogenesis. FASEB J (2008) 0.92
Fly cryptochrome and the visual system. Proc Natl Acad Sci U S A (2013) 0.91
MOBI: a web server to define and visualize structural mobility in NMR protein ensembles. Bioinformatics (2010) 0.91
Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci (2005) 0.91
Linear motifs in the C-terminus of D. melanogaster cryptochrome. Biochem Biophys Res Commun (2007) 0.89
Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics (2006) 0.89
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics (2005) 0.88
Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump. Cell Calcium (2007) 0.87
Protein sequence redundancy reduction: comparison of various method. Bioinformation (2010) 0.87
A novel WT1 gene mutation in a three-generation family with progressive isolated focal segmental glomerulosclerosis. Clin J Am Soc Nephrol (2010) 0.86
Bluues server: electrostatic properties of wild-type and mutated protein structures. Bioinformatics (2012) 0.85
Identification and in silico analysis of novel von Hippel-Lindau (VHL) gene variants from a large population. Ann Hum Genet (2011) 0.85
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures. Bioinformatics (2012) 0.85
CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures. Nucleic Acids Res (2005) 0.84
Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase. J Biol Chem (2005) 0.84
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J (2010) 0.84
Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. FEBS Lett (2008) 0.84
CDKN2A unclassified variants in familial malignant melanoma: combining functional and computational approaches for their assessment. Hum Mutat (2014) 0.84
A cry from the krill. Chronobiol Int (2010) 0.83
MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification. Protein Eng (2003) 0.83
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. BMC Bioinformatics (2013) 0.83
Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures. BMC Res Notes (2008) 0.83
A computational model of the LGI1 protein suggests a common binding site for ADAM proteins. PLoS One (2011) 0.83
Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy. Eur J Hum Genet (2012) 0.82
TESE: generating specific protein structure test set ensembles. Bioinformatics (2008) 0.82
Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues. Proc Natl Acad Sci U S A (2003) 0.81
Synthesis, Structure, and Reactivity of Model Complexes of Copper Nitrite Reductase. Inorg Chem (1996) 0.81
PANADA: protein association network annotation, determination and analysis. PLoS One (2013) 0.81
RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance. Amino Acids (2013) 0.81
Predictive bioinformatic identification of minor receptor group human rhinoviruses. FEBS Lett (2009) 0.79
Structural portrait of filamin interaction mechanisms. Curr Protein Pept Sci (2010) 0.79
Deletions and mutations in the acidic lipid-binding region of the plasma membrane Ca2+ pump: a study on different splicing variants of isoform 2. J Biol Chem (2010) 0.79
Computational approaches to protein-protein interaction. J Struct Funct Genomics (2003) 0.79
Correct machine learning on protein sequences: a peer-reviewing perspective. Brief Bioinform (2015) 0.79
Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq. PLoS One (2012) 0.78
Structural similarity between native proteins and chimera constructs obtained by inverting the amino Acid sequence. Acta Chim Slov (2010) 0.78
Immune roles of a rhamnose-binding lectin in the colonial ascidian Botryllus schlosseri. Immunobiology (2010) 0.78
Looking for putative phenoloxidases of compound ascidians: haemocyanin-like proteins in Polyandrocarpa misakiensis and Botryllus schlosseri. Dev Comp Immunol (2012) 0.77
In silico investigation of PHD-3 specific HIF1-α proline 567 hydroxylation: a new player in the VHL/HIF-1α interaction pathway? FEBS Lett (2013) 0.77
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures. BMC Struct Biol (2011) 0.77
Structural and functional characterization of the N-terminal domain of the yeast Mg2+ channel Mrs2. Acta Crystallogr D Biol Crystallogr (2013) 0.77
The G-M-N motif determines ion selectivity in the yeast magnesium channel Mrs2p. Metallomics (2013) 0.77
Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures. Curr Drug Discov Technol (2006) 0.76
Studying interactions by molecular dynamics simulations at high concentration. J Biomed Biotechnol (2012) 0.76
FELLS: Fast Estimator of Latent Local Structure. Bioinformatics (2017) 0.76
The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin. FEBS Open Bio (2013) 0.75
Electric dipole reorientation in the interaction of botulinum neurotoxins with neuronal membranes. FEBS Lett (2009) 0.75
Protein domain boundary predictions: a structural biology perspective. Open Biochem J (2009) 0.75
2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity. PLoS One (2013) 0.75
CARON--average RMSD of NMR structure ensembles. Bioinformation (2009) 0.75
Structural protein reorganization and fold emergence investigated through amino acid sequence permutations. Amino Acids (2014) 0.75