Published in Protein Sci on February 01, 2003
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Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol (2009) 3.01
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR (2005) 1.78
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR (2005) 1.62
Identification of helix capping and b-turn motifs from NMR chemical shifts. J Biomol NMR (2012) 1.12
PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res (2005) 1.12
PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Res (2003) 1.01
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Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins. J Biomol NMR (2007) 0.84
Backbone 1H, 13C and 15N assignments of the 25 kDa SPRY domain-containing SOCS box protein 2 (SSB-2). J Biomol NMR (2005) 0.83
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res (2015) 0.81
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An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR (2006) 0.79
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Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts. Biochim Biophys Acta (2015) 0.75
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids. J Biomol NMR (2011) 0.75
A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences. J Biomol NMR (2006) 0.75
Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts. J Biomol NMR (2016) 0.75
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Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC'). J Biomol NMR (2001) 0.81
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Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Mol Biochem Parasitol (2007) 1.86
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Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proc Natl Acad Sci U S A (2002) 1.73
Origin and evolution of new exons in rodents. Genome Res (2005) 1.57
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res (2005) 1.45
Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antivir Ther (2004) 1.41
Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics (2006) 1.27
Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol (2008) 1.19
Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect Immun (2010) 1.19
Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol (2007) 1.18
Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol (2004) 1.15
PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res (2005) 1.12
Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res (2003) 1.10
Functional annotation from predicted protein interaction networks. Bioinformatics (2005) 1.09
Enhanced functional information from predicted protein networks. Trends Biotechnol (2004) 1.04
Novel paradigms for drug discovery: computational multitarget screening. Trends Pharmacol Sci (2008) 1.03
PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Res (2003) 1.01
Accelerated protein structure comparison using TM-score-GPU. Bioinformatics (2012) 0.99
Structural and functional characterization of an organic hydroperoxide resistance protein from Mycoplasma gallisepticum. J Bacteriol (2008) 0.99
A novel knowledge-based approach to design inorganic-binding peptides. Bioinformatics (2007) 0.98
GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition. BMC Res Notes (2011) 0.97
Disguising itself--insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure. Mol Biochem Parasitol (2006) 0.97
Caries induced cytokine network in the odontoblast layer of human teeth. BMC Immunol (2011) 0.97
Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Struct Biol (2003) 0.95
FSSA: a novel method for identifying functional signatures from structural alignments. Bioinformatics (2005) 0.95
Identification of amino acids in the Dr adhesin required for binding to decay-accelerating factor. Mol Microbiol (2002) 0.94
Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antivir Ther (2005) 0.94
Protinfo PPC: a web server for atomic level prediction of protein complexes. Nucleic Acids Res (2009) 0.93
IGF1R variants associated with isolated single suture craniosynostosis. Am J Med Genet A (2011) 0.92
An enhanced Java graph applet interface for visualizing interactomes. Bioinformatics (2004) 0.92
Structural optimization and de novo design of dengue virus entry inhibitory peptides. PLoS Negl Trop Dis (2010) 0.90
Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Biomacromolecules (2012) 0.88
Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli. J Biol Chem (2006) 0.88
Structural insights into the cellular retinaldehyde-binding protein (CRALBP). Proteins (2005) 0.88
Computational representation of biological systems. Methods Mol Biol (2009) 0.88
Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation. Antivir Ther (2004) 0.87
Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides. Int J Oral Sci (2012) 0.86
Viral entry inhibitors block dengue antibody-dependent enhancement in vitro. Antiviral Res (2010) 0.86
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res (2005) 0.86
Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics (2010) 0.86
Genomic organization and sequence variation of the human integrin subunit alpha8 gene (ITGA8). Matrix Biol (2004) 0.86
The evolution and functional repertoire of translation proteins following the origin of life. Biol Direct (2010) 0.85
PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends Microbiol (2005) 0.85
The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. Protein Eng Des Sel (2006) 0.85
Heptad-repeat-2 mutations enhance the stability of the enfuvirtide-resistant HIV-1 gp41 hairpin structure. Antivir Ther (2005) 0.84
Identifying inhibitors of the SARS coronavirus proteinase. Bioorg Med Chem Lett (2003) 0.84
Probing the molecular mechanisms of quartz-binding peptides. Langmuir (2010) 0.84
Comment on "Evidence for positive epistasis in HIV-1". Science (2006) 0.83
The Bioverse API and web application. Methods Mol Biol (2009) 0.83
Identification of potential HIV-1 targets of minocycline. Bioinformatics (2007) 0.83
A knowledge-based scoring function based on residue triplets for protein structure prediction. Protein Eng Des Sel (2006) 0.82
A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins (2009) 0.82
Prediction and integration of regulatory and protein-protein interactions. Methods Mol Biol (2009) 0.82
Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. AIDS (2004) 0.82
Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Struct Biol (2008) 0.82
Solution study of engineered quartz binding peptides using replica exchange molecular dynamics. Biomacromolecules (2010) 0.81
Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol (2009) 0.81
An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR (2006) 0.79
Automated functional classification of experimental and predicted protein structures. BMC Bioinformatics (2006) 0.79
A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction. Proteins (2009) 0.79
Diversity of protein structures and difficulties in fold recognition: the curious case of protein G. F1000 Biol Rep (2009) 0.79
Scoring functions for de novo protein structure prediction revisited. Methods Mol Biol (2008) 0.79
Identification of potential multitarget antimalarial drugs. JAMA (2005) 0.78
Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics. AIDS (2005) 0.78
Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin. PLoS One (2013) 0.78
A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit Lett (2010) 0.78
INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics (2006) 0.78
Disease risk of missense mutations using structural inference from predicted function. Curr Protein Pept Sci (2010) 0.77
Structure prediction of partial-length protein sequences. Int J Mol Sci (2013) 0.77
Weak agreement between Antivirogram and Phenosense assays in predicting reduced susceptibility to antiretroviral drugs. J Clin Microbiol (2004) 0.77
Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. BMC Plant Biol (2013) 0.76
The enzymatic and metabolic capabilities of early life. PLoS One (2012) 0.76
Inferring molecular interactions pathways from eQTL data. Methods Mol Biol (2009) 0.76
HIV-1 genotypic drug-resistance interpretation algorithms need to include hypersusceptibility-associated mutations. J Infect Dis (2004) 0.75
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics (2011) 0.75