Published in BMC Bioinformatics on July 12, 2006
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
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Vaccinia virus proteins A52 and B14 Share a Bcl-2-like fold but have evolved to inhibit NF-kappaB rather than apoptosis. PLoS Pathog (2008) 1.57
The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study. PLoS One (2014) 1.45
Synergistic antimicrotubule therapy for prostate cancer. Biochem Pharmacol (2010) 1.44
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol (2009) 1.43
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics (2009) 1.30
Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry (2009) 1.30
Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Mol Cells (2009) 1.27
Evolutionary mix-and-match with MFS transporters. Proc Natl Acad Sci U S A (2013) 1.26
Signal transducing membrane complexes of photoreceptor outer segments. Vision Res (2008) 1.25
Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA. Appl Environ Microbiol (2010) 1.22
The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem (2009) 1.21
Enhancing UCSF Chimera through web services. Nucleic Acids Res (2014) 1.09
Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease. Hum Mutat (2013) 1.07
Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers. Proc Natl Acad Sci U S A (2012) 1.06
The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme. RNA (2008) 1.02
Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis. Proc Natl Acad Sci U S A (2011) 1.00
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Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2014) 0.95
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Human bocavirus capsid structure: insights into the structural repertoire of the parvoviridae. J Virol (2010) 0.93
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Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Comput Biol (2011) 0.89
Plasmodium falciparum UvrD helicase translocates in 3' to 5' direction, colocalizes with MLH and modulates its activity through physical interaction. PLoS One (2012) 0.89
Domain organization of membrane-bound factor VIII. Biopolymers (2013) 0.87
Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex. Proc Natl Acad Sci U S A (2013) 0.87
Structural mechanism for the regulation of HCN ion channels by the accessory protein TRIP8b. Structure (2015) 0.87
Evolutionarily conserved structural changes in phosphatidylinositol 5-phosphate 4-kinase (PI5P4K) isoforms are responsible for differences in enzyme activity and localization. Biochem J (2013) 0.86
Structural and functional characterization of the Streptococcus pneumoniae RrgB pilus backbone D1 domain. J Biol Chem (2011) 0.85
Integrated visual analysis of protein structures, sequences, and feature data. BMC Bioinformatics (2015) 0.84
A divergent variant of Grapevine leafroll-associated virus 3 is present in California. Virol J (2012) 0.84
Interactions of laminin β3 fragment with β1-integrin receptor: A revisit of the apical ectoplasmic specialization-blood-testis-barrier-hemidesmosome functional axis in the testis. Spermatogenesis (2011) 0.83
Autophosphorylation-induced degradation of the Pho85 cyclin Pcl5 is essential for response to amino acid limitation. Mol Cell Biol (2008) 0.83
The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. PLoS Comput Biol (2014) 0.83
Modulation of the FGF14:FGF14 homodimer interaction through short peptide fragments. CNS Neurol Disord Drug Targets (2014) 0.82
A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. J Cell Biol (2015) 0.82
Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. J Mol Model (2011) 0.82
Assembly of the novel five-component apicomplexan multi-aminoacyl-tRNA synthetase complex is driven by the hybrid scaffold protein Tg-p43. PLoS One (2014) 0.81
Identification of potential Plk1 targets in a cell-cycle specific proteome through structural dynamics of kinase and Polo box-mediated interactions. PLoS One (2013) 0.81
Enhanced degradation of dihydrofolate reductase through inhibition of NAD kinase by nicotinamide analogs. Mol Pharmacol (2012) 0.81
Minor modifications of the C-terminal helix reschedule the favored chemical reactions catalyzed by theta class glutathione transferase T1-1. J Biol Chem (2009) 0.81
Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct Integr Genomics (2011) 0.80
The apical ectoplasmic specialization-blood-testis barrier functional axis is a novel target for male contraception. Adv Exp Med Biol (2012) 0.80
Crystal structures of archaemetzincin reveal a moldable substrate-binding site. PLoS One (2012) 0.80
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption. PLoS Comput Biol (2015) 0.80
Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification. Mol Cell Proteomics (2015) 0.79
The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes. Nucleic Acids Res (2015) 0.79
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Integrative visual analysis of protein sequence mutations. BMC Proc (2014) 0.79
Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins. Chem Phys (2014) 0.79
Identification of Navβ1 residues involved in the modulation of the sodium channel Nav1.4. PLoS One (2013) 0.78
Examination of the subsarcolemmal tubular system of mammalian skeletal muscle fibers. Biophys J (2013) 0.78
Monoamine neurotransmitters as substrates for novel tick sulfotransferases, homology modeling, molecular docking, and enzyme kinetics. ACS Chem Biol (2010) 0.78
In silico analysis of missense mutations in LPAR6 reveals abnormal phospholipid signaling pathway leading to hypotrichosis. PLoS One (2014) 0.78
Examination of mechanism of N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB) reveals unexpected role for dynamic tyrosine. J Biol Chem (2012) 0.78
Stereocilia-staircase spacing is influenced by myosin III motors and their cargos espin-1 and espin-like. Nat Commun (2016) 0.78
Synthesis and antileukemic activities of C1-C10-modified parthenolide analogues. Bioorg Med Chem (2015) 0.78
Computational modeling study of human nicotinic acetylcholine receptor for developing new drugs in the treatment of alcoholism. Interdiscip Sci (2009) 0.77
An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization. G3 (Bethesda) (2015) 0.77
Suppressor mutations suggest a surface on PAT-4 (Integrin-linked Kinase) that interacts with UNC-112 (Kindlin). J Biol Chem (2014) 0.76
Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. J Comput Aided Mol Des (2012) 0.76
Understanding Dengue Virus Capsid Protein Interaction with Key Biological Targets. Sci Rep (2015) 0.76
Viral interference with functions of the cellular receptor tyrosine phosphatase CD45. Viruses (2015) 0.76
Genetic diversity of hemagglutinin gene of A(H1N1)pdm09 influenza strains isolated in Taiwan and its potential impact on HA-neutralizing epitope interaction. Hum Vaccin Immunother (2014) 0.76
Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. Biochemistry (2014) 0.76
High diversification of CD94 by alternative splicing in New World primates. Immunogenetics (2013) 0.75
Suggestion of suitable animal models for in vivo studies of protein tyrosine phosphatase 1b (PTP1B) inhibitors using computational approaches. Springerplus (2014) 0.75
Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia. Genet Mol Biol (2012) 0.75
Cytochrome P450 125A4, the Third Cholesterol C-26 Hydroxylase from Mycobacterium smegmatis. Biochemistry (2015) 0.75
Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures. Acta Crystallogr F Struct Biol Commun (2015) 0.75
Molecular Basis of Transient Neonatal Zinc Deficiency: NOVEL ZnT2 MUTATIONS DISRUPTING ZINC BINDING AND PERMEATION. J Biol Chem (2016) 0.75
Antiviral screening identifies adenosine analogs targeting the endogenous dsRNA Leishmania RNA virus 1 (LRV1) pathogenicity factor. Proc Natl Acad Sci U S A (2017) 0.75
Structures of potent anticancer compounds bound to tubulin. Protein Sci (2015) 0.75
Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1). Comput Struct Biotechnol J (2015) 0.75
Heme-based catalytic properties of human serum albumin. Cell Death Discov (2015) 0.75
Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J (2015) 0.75
Structural basis for inhibition of the MDM2:p53 interaction by an optimized MDM2-binding peptide selected with mRNA display. PLoS One (2014) 0.75
Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow. Bioinformation (2011) 0.75
The myelin oligodendrocyte glycoprotein directly binds nerve growth factor to modulate central axon circuitry. J Cell Biol (2015) 0.75
In silico identification of potential inhibitors targeting Streptococcus mutans sortase A. Int J Oral Sci (2017) 0.75
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. Acta Crystallogr D Biol Crystallogr (2012) 0.75
Single-binding mode integration of hemicellulose degrading enzymes via adaptor scaffoldins in Ruminococcus flavefaciens cellulosome. J Biol Chem (2016) 0.75
Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proc Natl Acad Sci U S A (2017) 0.75
Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models. Proc Natl Acad Sci U S A (2017) 0.75
Strain-dependent neutralization reveals antigenic variation of human parechovirus 3. Sci Rep (2017) 0.75
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Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci (2004) 1.39
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Multiple Alignment of protein structures and sequences for VMD. Bioinformatics (2005) 1.23
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Visualizing density maps with UCSF Chimera. J Struct Biol (2006) 5.75
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Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2010) 2.96
DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry (2006) 2.65
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UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol (2011) 2.10
Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci U S A (2003) 2.03
Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics (2003) 1.79
Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics (2002) 1.57
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Comparison of human solute carriers. Protein Sci (2010) 1.29
The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. J Pharmacol Exp Ther (2008) 1.23
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Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem Biol (2006) 1.12
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics (2010) 1.09
Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res (2006) 1.07
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics (2003) 1.06
Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4). Pharmacogenet Genomics (2007) 1.02
Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1. Pharmacogenetics (2003) 1.01
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Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenet Genomics (2005) 0.86
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Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates. Am J Physiol Renal Physiol (2010) 0.81
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Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2. Drug Metab Dispos (2005) 0.79
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SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Pac Symp Biocomput (2003) 0.77
Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol (2012) 0.77
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