Published in Methods Mol Biol on January 01, 2007
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res (2005) 4.32
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50
Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat (2009) 3.14
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics (2004) 2.16
BaCelLo: a balanced subcellular localization predictor. Bioinformatics (2006) 2.14
PredGPI: a GPI-anchor predictor. BMC Bioinformatics (2008) 1.86
A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics (2008) 1.73
SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst (2011) 1.53
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49
Predicting protein stability changes from sequences using support vector machines. Bioinformatics (2005) 1.46
Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform (2009) 1.44
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics (2003) 1.44
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network. Proteomics (2004) 1.20
An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics (2010) 1.18
WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics (2013) 1.14
In silico prediction of the structure of membrane proteins: is it feasible? Brief Bioinform (2003) 1.13
Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.10
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res (2006) 1.10
The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief Funct Genomic Proteomic (2008) 1.10
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics (2005) 1.09
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng (2002) 1.09
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci (2003) 1.08
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics (2008) 1.08
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics (2003) 1.07
EX-HOM (EXome HOMozygosity): a proof of principle. Hum Hered (2011) 1.06
A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics (2012) 1.05
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res (2010) 0.99
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res (2011) 0.99
The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res (2009) 0.96
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinformatics (2011) 0.94
Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome. Hum Mutat (2011) 0.94
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics (2009) 0.91
Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics (2008) 0.89
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics (2012) 0.87
The pros and cons of predicting protein contact maps. Methods Mol Biol (2008) 0.87
Retracted Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy. Protein Sci (2002) 0.87
MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res (2011) 0.87
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinformatics (2011) 0.86
New functions of an old protein: the eukaryotic porin or voltage dependent anion selective channel (VDAC). Ital J Biochem (2003) 0.86
Role of the C-terminus of Pleurotus eryngii Ery4 laccase in determining enzyme structure, catalytic properties and stability. Protein Eng Des Sel (2012) 0.86
Evolution of detoxifying systems: the role of environment and population history in shaping genetic diversity at human CYP2D6 locus. Pharmacogenet Genomics (2010) 0.84
MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinformatics (2013) 0.83
A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues. Proteins (2004) 0.83
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy. Protein Sci (2003) 0.82
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinformatics (2013) 0.82
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. BMC Genomics (2015) 0.81
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. Bioinformatics (2011) 0.81
Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies. Biopolymers (2002) 0.81
Predicting cancer-associated germline variations in proteins. BMC Genomics (2012) 0.81
Functional characterization of a second porin isoform in Drosophila melanogaster. DmPorin2 forms voltage-independent cation-selective pores. J Biol Chem (2004) 0.80
3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering. Biophys J (2003) 0.80
A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus. Protein Eng (2002) 0.80
Fast overlapping of protein contact maps by alignment of eigenvectors. Bioinformatics (2010) 0.80
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinformatics (2013) 0.80
Frataxin mRNA isoforms in FRDA patients and normal subjects: effect of tocotrienol supplementation. Biomed Res Int (2013) 0.80
Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study. Mol Membr Biol (2005) 0.80
Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme. Biochim Biophys Acta (2006) 0.80
Is there an optimal substitution matrix for contact prediction with correlated mutations? IEEE/ACM Trans Comput Biol Bioinform (2011) 0.79
Weather factors influencing the population dynamics of Culex pipiens (Diptera: Culicidae) in the Po Plain Valley, Italy (1997-2011). Environ Entomol (2014) 0.79
Expression of different forms of transglutaminases by immature cells of Helianthus tuberosus sprout apices. Amino Acids (2012) 0.79
Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure. BioData Min (2011) 0.79
Plant and animal transglutaminases: do similar functions imply similar structures? Amino Acids (2008) 0.78
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. Bioinformatics (2013) 0.78
A computational approach for detecting peptidases and their specific inhibitors at the genome level. BMC Bioinformatics (2007) 0.78
Thermodynamics of binding of regulatory ligands to tissue transglutaminase. Amino Acids (2009) 0.78
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. Bioinformatics (2013) 0.78
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol Biol (2009) 0.78
Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature. Archaea (2005) 0.78
Haplotype of single nucleotide polymorphisms in exon 6 of the MZF-1 gene and Alzheimer's disease. J Alzheimers Dis (2013) 0.77
Histone deacetylase 1: a target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer. J Lipid Res (2005) 0.77
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinformatics (2012) 0.77
Generation of diversity by somatic mutation in the Camelus dromedarius T-cell receptor gamma variable domains. Eur J Immunol (2012) 0.77
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. Database (Oxford) (2013) 0.77
Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes. J Proteome Res (2007) 0.77