Published in Bioinformatics on October 04, 2005
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Designing and benchmarking the MULTICOM protein structure prediction system. BMC Struct Biol (2013) 0.88
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Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. Structure (2015) 0.84
ProQ2: estimation of model accuracy implemented in Rosetta. Bioinformatics (2016) 0.83
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics (2008) 0.83
Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors. BMC Cancer (2015) 0.81
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Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures. J Struct Funct Genomics (2012) 0.80
Bioinformatic analysis of pathogenic missense mutations of activin receptor like kinase 1 ectodomain. PLoS One (2011) 0.80
Molecular docking simulations provide insights in the substrate binding sites and possible substrates of the ABCC6 transporter. PLoS One (2014) 0.79
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Cloning of interleukin-10 from African clawed frog (Xenopus tropicalis), with the Finding of IL-19/20 homologue in the IL-10 locus. J Immunol Res (2015) 0.76
From local structure to a global framework: recognition of protein folds. J R Soc Interface (2014) 0.76
Predicting the molecular interactions of CRIP1a-cannabinoid 1 receptor with integrated molecular modeling approaches. Bioorg Med Chem Lett (2014) 0.76
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3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
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TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res (2009) 3.45
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci (2004) 3.40
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Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics (2002) 2.66
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Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55
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Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins (2007) 2.50
Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci (2006) 2.39
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics (2008) 2.38
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol (2006) 2.27
Domain rearrangements in protein evolution. J Mol Biol (2005) 2.12
All are not equal: a benchmark of different homology modeling programs. Protein Sci (2005) 1.99
Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol (2005) 1.95
Expansion of protein domain repeats. PLoS Comput Biol (2006) 1.93
LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins (2003) 1.90
Arrangements in the modular evolution of proteins. Trends Biochem Sci (2008) 1.78
A study of the membrane-water interface region of membrane proteins. J Mol Biol (2004) 1.68
Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci (2008) 1.56
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins (2009) 1.48
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins (2003) 1.46
Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature (2012) 1.42
Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol (2007) 1.39
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
Pcons.net: protein structure prediction meta server. Nucleic Acids Res (2007) 1.28
Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins (2009) 1.28
Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol (2006) 1.27
ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics (2006) 1.24
In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol (2003) 1.21
Preferential attachment in the evolution of metabolic networks. BMC Genomics (2005) 1.20
Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci (2014) 1.13
Identifying and quantifying orphan protein sequences in fungi. J Mol Biol (2009) 1.11
Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci (2002) 1.10
PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics (2013) 1.09
Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J Mol Biol (2009) 1.07
Using evolutionary information for the query and target improves fold recognition. Proteins (2004) 1.07
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. Bioinformatics (2012) 1.03
Coils in the membrane core are conserved and functionally important. J Mol Biol (2008) 1.03
Why are polar residues within the membrane core evolutionary conserved? Proteins (2010) 1.02
Tertiary windowing to detect positive diversifying selection. J Mol Evol (2005) 1.01
Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol (2007) 1.00
Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics (2008) 1.00
Repositioning of transmembrane alpha-helices during membrane protein folding. J Mol Biol (2010) 0.97
Nebulin: a study of protein repeat evolution. J Mol Biol (2010) 0.97
Rapid membrane protein topology prediction. Bioinformatics (2011) 0.97
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics (2005) 0.94
Protein expansion is primarily due to indels in intrinsically disordered regions. Mol Biol Evol (2013) 0.94
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinformatics (2010) 0.90
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (2013) 0.88
The impact of splicing on protein domain architecture. Curr Opin Struct Biol (2013) 0.87
A guideline to proteome-wide α-helical membrane protein topology predictions. Proteomics (2012) 0.86
Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. J Mol Biol (2012) 0.86
Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci (2007) 0.85
The evolution of filamin-a protein domain repeat perspective. J Struct Biol (2012) 0.85
An introduction to membrane proteins. J Proteome Res (2011) 0.85
Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol (2010) 0.84
Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins. Biochim Biophys Acta (2013) 0.83
Remote homology detection of integral membrane proteins using conserved sequence features. Proteins (2008) 0.81
The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity. Gastroenterology (2011) 0.81
Manipulating the genetic code for membrane protein production: what have we learnt so far? Biochim Biophys Acta (2011) 0.81
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinformatics (2006) 0.81
Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. Bioinformatics (2012) 0.79
Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci (2010) 0.78
Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins (2014) 0.77
Improved predictions by Pcons.net using multiple templates. Bioinformatics (2010) 0.77
Ligand binding properties of human galanin receptors. Mol Membr Biol (2012) 0.76
KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics (2011) 0.76
Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. ACS Synth Biol (2015) 0.75
Determining receptor-ligand interaction of human galanin receptor type 3. Neurochem Int (2010) 0.75
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Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods Mol Biol (2013) 0.75
Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics (2013) 0.75