Published in Nucleic Acids Res on December 03, 2013
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Protein Repeats from First Principles. Sci Rep (2016) 0.77
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PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. Nucleic Acids Res (2015) 0.77
Statistical analysis of structural determinants for protein-DNA-binding specificity. Proteins (2016) 0.76
The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res (2017) 0.76
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Role of mRNA structure in the control of protein folding. Nucleic Acids Res (2016) 0.76
ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier. Biomed Res Int (2016) 0.76
The origin of β-strand bending in globular proteins. BMC Struct Biol (2015) 0.75
Topological knots and links in proteins. Proc Natl Acad Sci U S A (2017) 0.75
The Evolution of Function within the Nudix homology Clan. Proteins (2016) 0.75
Complete fold annotation of the human proteome using a novel structural feature space. Sci Rep (2017) 0.75
Addressing inaccuracies in BLOSUM computation improves homology search performance. BMC Bioinformatics (2016) 0.75
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. BMC Bioinformatics (2016) 0.75
Benchmarking the next generation of homology inference tools. Bioinformatics (2016) 0.75
Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools. Pharmacognosy Res (2015) 0.75
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PLoS Comput Biol (2015) 0.75
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. Proteins (2016) 0.75
A novel index of protein-protein interface propensity improves interface residue recognition. BMC Syst Biol (2016) 0.75
Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms. Comput Struct Biotechnol J (2015) 0.75
BCSearch: fast structural fragment mining over large collections of protein structures. Nucleic Acids Res (2015) 0.75
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification. Front Microbiol (2017) 0.75
Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core. Proc Natl Acad Sci U S A (2017) 0.75
bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. J Cheminform (2016) 0.75
Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. Archaea (2016) 0.75
The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophys J (2017) 0.75
Impact of structure space continuity on protein fold classification. Sci Rep (2016) 0.75
Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Proteins (2016) 0.75
Identifying the missing proteins in human proteome by biological language model. BMC Syst Biol (2016) 0.75
Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix. J Struct Funct Genomics (2017) 0.75
The Ramachandran Number: An Order Parameter for Protein Geometry. PLoS One (2016) 0.75
The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone. Protein Sci (2015) 0.75
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. Structure (2016) 0.75
In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality. Int J Mol Sci (2016) 0.75
Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures. Biomolecules (2015) 0.75
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval. Sci Rep (2015) 0.75
Misannotation Awareness: A Tale of Two Gene-Groups. Front Plant Sci (2016) 0.75
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PLoS Comput Biol (2016) 0.75
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. BMC Bioinformatics (2016) 0.75
A multiparametric computational algorithm for comprehensive assessment of genetic mutations in mucopolysaccharidosis type IIIA (Sanfilippo syndrome). PLoS One (2015) 0.75
Aromatic claw: A new fold with high aromatic content that evades structural prediction. Protein Sci (2016) 0.75
Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein. Pharmacognosy Res (2015) 0.75
Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. Sci Rep (2015) 0.75
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. Bioinform Biol Insights (2015) 0.75
CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area. PLoS One (2015) 0.75
Structure-based prediction and identification of 4-epimerization activity of phosphate sugars in class II aldolases. Sci Rep (2017) 0.75
Protein structural motifs in prediction and design. Curr Opin Struct Biol (2017) 0.75
An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h). PeerJ (2017) 0.75
Elastic network model of learned maintained contacts to predict protein motion. PLoS One (2017) 0.75
The Enigmatic Origin of Papillomavirus Protein Domains. Viruses (2017) 0.75
Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol (2017) 0.75
A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase. PLoS One (2017) 0.75
Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. Front Microbiol (2017) 0.75
An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins. PLoS One (2017) 0.75
A distance geometry-based description and validation of protein main-chain conformation. IUCrJ (2017) 0.75
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The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res (2000) 11.38
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SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07
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WebLogo: a sequence logo generator. Genome Res (2004) 59.58
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SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
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The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
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Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature (2007) 7.12
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A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
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Sulfotransferases and sulfatases in mycobacteria. Chem Biol (2002) 1.74
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins (2005) 1.71
Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell (2009) 1.52
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Res (2004) 1.43
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Automated multi-model reconstruction from single-particle electron microscopy data. J Struct Biol (2010) 1.18
Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics (2005) 1.16
A method for the alignment of heterogeneous macromolecules from electron microscopy. J Struct Biol (2008) 1.16
Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res (2011) 1.10
An alternative model of amino acid replacement. Bioinformatics (2004) 1.10
A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins (2005) 1.09
Newborn screening for SCID identifies patients with ataxia telangiectasia. J Clin Immunol (2012) 1.05
Protein secondary structure: entropy, correlations and prediction. Bioinformatics (2004) 1.04
Target selection and deselection at the Berkeley Structural Genomics Center. Proteins (2006) 0.98
Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics (2005) 0.97
Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. J Mol Biol (2004) 0.93
Measurements of protein sequence-structure correlations. Proteins (2004) 0.90
Pairwise alignment incorporating dipeptide covariation. Bioinformatics (2005) 0.89
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics (2007) 0.88
Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A (2009) 0.86
Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PLoS One (2011) 0.85
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Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation. J Clin Immunol (2015) 0.82
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Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pac Symp Biocomput (2015) 0.82
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High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res (2012) 0.80
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Alignment-free local structural search by writhe decomposition. Bioinformatics (2010) 0.79
Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. Proteins (2013) 0.78
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A continuous fluorescence assay for the characterization of Nudix hydrolases. Anal Biochem (2013) 0.77
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Optimal and fast rotational alignment of volumes with missing data in Fourier space. J Struct Biol (2013) 0.75