Published in Bioinformatics on May 07, 2009
The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc (2015) 8.53
Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res (2013) 4.24
Protein annotation and modelling servers at University College London. Nucleic Acids Res (2010) 3.77
Whole-genome sequence of Schistosoma haematobium. Nat Genet (2012) 2.91
A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics (2011) 2.34
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VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses. J Exp Med (2011) 1.77
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat Genet (2016) 1.55
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Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet (2015) 1.46
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Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci U S A (2013) 1.11
Using amino acid physicochemical distance transformation for fast protein remote homology detection. PLoS One (2012) 1.10
Plasmids with a chromosome-like role in rhizobia. J Bacteriol (2011) 1.07
Defining sequence space and reaction products within the cyanuric acid hydrolase (AtzD)/barbiturase protein family. J Bacteriol (2012) 1.04
Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes. Cell Microbiol (2014) 1.02
Human 1-acylglycerol-3-phosphate O-acyltransferase isoforms 1 and 2: biochemical characterization and inability to rescue hepatic steatosis in Agpat2(-/-) gene lipodystrophic mice. J Biol Chem (2011) 1.01
Protein remote homology detection by combining Chou's distance-pair pseudo amino acid composition and principal component analysis. Mol Genet Genomics (2015) 1.00
Plant pathogenic bacteria utilize biofilm growth-associated repressor (BigR), a novel winged-helix redox switch, to control hydrogen sulfide detoxification under hypoxia. J Biol Chem (2011) 0.99
CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics (2014) 0.98
Lipid droplet-associated proteins are involved in the biosynthesis and hydrolysis of triacylglycerol in Mycobacterium bovis bacillus Calmette-Guerin. J Biol Chem (2010) 0.96
Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput Biol (2012) 0.95
Detection of the Wolbachia protein WPIP0282 in mosquito spermathecae: implications for cytoplasmic incompatibility. Insect Biochem Mol Biol (2013) 0.94
Mutations in the GlyT2 gene (SLC6A5) are a second major cause of startle disease. J Biol Chem (2012) 0.93
Dietary isothiocyanate-induced apoptosis via thiol modification of DNA topoisomerase IIα. J Biol Chem (2011) 0.92
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res (2014) 0.90
A wheat SIMILAR TO RCD-ONE gene enhances seedling growth and abiotic stress resistance by modulating redox homeostasis and maintaining genomic integrity. Plant Cell (2014) 0.88
Deletion and gene expression analyses define the paxilline biosynthetic gene cluster in Penicillium paxilli. Toxins (Basel) (2013) 0.88
Identification of a Plasmodium falciparum phospholipid transfer protein. J Biol Chem (2013) 0.87
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des (2013) 0.86
A leucine-rich repeat assembly approach for homology modeling of the human TLR5-10 and mouse TLR11-13 ectodomains. J Mol Model (2010) 0.85
Engagement of nucleotide-binding oligomerization domain-containing protein 1 (NOD1) by receptor-interacting protein 2 (RIP2) is insufficient for signal transduction. J Biol Chem (2014) 0.85
eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One (2012) 0.85
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. BMC Bioinformatics (2015) 0.84
Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. Nucleic Acids Res (2015) 0.83
Octarellin VI: using rosetta to design a putative artificial (β/α)8 protein. PLoS One (2013) 0.82
Insights into SCP/TAPS proteins of liver flukes based on large-scale bioinformatic analyses of sequence datasets. PLoS One (2012) 0.82
S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Front Microbiol (2015) 0.82
Blockade of islet amyloid polypeptide fibrillation and cytotoxicity by the secretory chaperones 7B2 and proSAAS. FEBS Lett (2013) 0.81
Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet (2013) 0.80
nfxB as a novel target for analysis of mutation spectra in Pseudomonas aeruginosa. PLoS One (2013) 0.80
Prediction of bioluminescent proteins using auto covariance transformation of evolutional profiles. Int J Mol Sci (2012) 0.80
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallogr D Struct Biol (2016) 0.80
Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinformatics (2014) 0.80
Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids. PLoS One (2011) 0.79
Outer membrane proteins can be simply identified using secondary structure element alignment. BMC Bioinformatics (2011) 0.79
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct (2015) 0.79
Ultraviolet and 5'fluorodeoxyuridine induced random mutagenesis in Chlorella vulgaris and its impact on fatty acid profile: a new insight on lipid-metabolizing genes and structural characterization of related proteins. Mar Biotechnol (NY) (2014) 0.78
The retroviral cyclin of walleye dermal sarcoma virus binds cyclin-dependent kinases 3 and 8. Virology (2010) 0.78
Oligomerization mechanisms of an H-NS family protein, Pmr, encoded on the plasmid pCAR1 provide a molecular basis for functions of H-NS family members. PLoS One (2014) 0.78
A network-based approach to identify substrate classes of bacterial glycosyltransferases. BMC Genomics (2014) 0.78
Computational analysis predicts the Kaposi's sarcoma-associated herpesvirus tegument protein ORF63 to be alpha helical. Proteins (2012) 0.78
TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets. Parasit Vectors (2013) 0.77
BioShell-Threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinformatics (2014) 0.77
TMFoldWeb: a web server for predicting transmembrane protein fold class. Biol Direct (2015) 0.77
Predicting the molecular interactions of CRIP1a-cannabinoid 1 receptor with integrated molecular modeling approaches. Bioorg Med Chem Lett (2014) 0.76
Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis. Proteins (2016) 0.76
Structure based annotation of Helicobacter pylori strain 26695 proteome. PLoS One (2014) 0.76
Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J (2017) 0.75
A homology model for Clostridium difficile methionyl tRNA synthetase: active site analysis and docking interactions. J Mol Model (2010) 0.75
A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides. J Biol Chem (2016) 0.75
Cysteine-Rich Atrial Secretory Protein from the Snail Achatina achatina: Purification and Structural Characterization. PLoS One (2015) 0.75
Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein. Biol Chem (2012) 0.75
Structural modeling of the N-terminal signal-receiving domain of IκBα. Front Mol Biosci (2015) 0.75
Identification of the catalytic ubiquinone-binding site of Vibrio cholerae sodium-dependent NADH dehydrogenase: a novel ubiquinone-binding motif. J Biol Chem (2017) 0.75
Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci (2013) 0.75
Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms. BMC Res Notes (2015) 0.75
Glutamate Transporter Homolog-based Model Predicts That Anion-π Interaction Is the Mechanism for the Voltage-dependent Response of Prestin. J Biol Chem (2015) 0.75
Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A. PLoS One (2016) 0.75
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol (2017) 0.75
Protein structure prediction servers at University College London. Nucleic Acids Res (2005) 6.70
The DISOPRED server for the prediction of protein disorder. Bioinformatics (2004) 5.98
Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics (2009) 4.67
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res (2013) 4.24
K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol (2012) 4.00
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics (2003) 3.70
Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc Natl Acad Sci U S A (2004) 3.39
BioRAT: extracting biological information from full-length papers. Bioinformatics (2004) 2.63
Classification of intrinsically disordered regions and proteins. Chem Rev (2014) 2.48
Effect of APOE ε4 status on intrinsic network connectivity in cognitively normal elderly subjects. Arch Neurol (2011) 2.40
Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci (2002) 2.20
Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol (2003) 2.16
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A (2012) 2.02
Amyloid-first and neurodegeneration-first profiles characterize incident amyloid PET positivity. Neurology (2013) 1.74
A nonsense mutation in COQ9 causes autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency: a potentially treatable form of mitochondrial disease. Am J Hum Genet (2009) 1.71
Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics (2005) 1.70
Cloning and Expression of a Clostridium acetobutylicum Alcohol Dehydrogenase Gene in Escherichia coli. Appl Environ Microbiol (1988) 1.63
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
Inferring function using patterns of native disorder in proteins. PLoS Comput Biol (2007) 1.56
Statistical SPECT processing in MRI-negative epilepsy surgery. Neurology (2014) 1.46
Predicting metal-binding site residues in low-resolution structural models. J Mol Biol (2004) 1.42
Identification of the sources of fecal coliforms in an urban watershed using antibiotic resistance analysis. Water Res (2002) 1.39
Public participation in soil surveys: lessons from a pilot study in England. Environ Sci Technol (2012) 1.31
Protein topology from predicted residue contacts. Protein Sci (2011) 1.25
Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. PLoS Comput Biol (2010) 1.24
Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinformatics (2012) 1.22
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics (2009) 1.18
Prediction of contacts from correlated sequence substitutions. Curr Opin Struct Biol (2013) 1.16
Evaluation of predictions in the CASP10 model refinement category. Proteins (2014) 1.15
Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci (2007) 1.14
Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One (2011) 1.12
FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. Hum Mol Genet (2010) 1.08
Disrupted thalamocortical connectivity in PSP: a resting-state fMRI, DTI, and VBM study. Parkinsonism Relat Disord (2011) 1.08
Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol (2009) 1.08
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics (2013) 1.07
The transmembrane topology of Batten disease protein CLN3 determined by consensus computational prediction constrained by experimental data. FEBS Lett (2008) 1.03
ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res (2008) 1.03
The alien limb phenomenon. J Neurol (2013) 1.01
Resting state functional MRI in Alzheimer's Disease. Alzheimers Res Ther (2012) 0.99
Structural constraints on the covariance matrix derived from multiple aligned protein sequences. PLoS One (2011) 0.99
De novo backbone scaffolds for protein design. Proteins (2010) 0.98
Modularity of intrinsic disorder in the human proteome. Proteins (2010) 0.98
The contribution of intrinsic disorder prediction to the elucidation of protein function. Curr Opin Struct Biol (2013) 0.98
FFPred 2.0: improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences. PLoS One (2013) 0.98
Benchmarking secondary structure prediction for fold recognition. Proteins (2003) 0.97
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res (2004) 0.96
The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics (2011) 0.96
Towards genome-scale structure prediction for transmembrane proteins. Philos Trans R Soc Lond B Biol Sci (2006) 0.93
Statistical parametric mapping demonstrates asymmetric uptake with Tc-99m ECD and Tc-99m HMPAO SPECT in normal brain. J Cereb Blood Flow Metab (2011) 0.91
Docking protein domains in contact space. BMC Bioinformatics (2006) 0.91
springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'. Bioinformatics (2006) 0.89
Targeting novel folds for structural genomics. Proteins (2002) 0.89
A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS One (2008) 0.88
Membrane protein structural bioinformatics. J Struct Biol (2011) 0.86
Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration. J Mol Biol (2011) 0.86
Improving classification in protein structure databases using text mining. BMC Bioinformatics (2009) 0.85
Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. Comput Biol Chem (2011) 0.85
High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics (2006) 0.85
The genomic threading database. Bioinformatics (2004) 0.83
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics (2008) 0.83
On mind wandering, attention, brain networks, and meditation. Explore (NY) (2013) 0.81
Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics (2013) 0.80
Re-evaluating the "rules" of protein topology. J Comput Biol (2010) 0.80
Computational resources for the prediction and analysis of native disorder in proteins. Methods Mol Biol (2010) 0.79
An automatic method for assessing structural importance of amino acid positions. BMC Struct Biol (2009) 0.78
FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. Hum Mol Genet (2015) 0.78
Analytic markovian rates for generalized protein structure evolution. PLoS One (2012) 0.76
Neurodegeneration, Konigsberg, and the New York City subway: dementia researchers on edge(s). Neurology (2013) 0.75
Prediction of protein contacts from correlated sequence substitutions. Sci Prog (2013) 0.75
Pathophysiology of language, speech and emotions in neurodegenerative disease. Parkinsonism Relat Disord (2014) 0.75
A neurological complication of a uterine fibroid. Neurocrit Care (2013) 0.75
From chemical risk assessment to environmental quality management: the challenge for soil protection. Environ Sci Technol (2010) 0.75