Published in BMC Bioinformatics on January 14, 2013
An Evolutionary View on Disulfide Bond Connectivities Prediction Using Phylogenetic Trees and a Simple Cysteine Mutation Model. PLoS One (2015) 0.79
Soft Computing Methods for Disulfide Connectivity Prediction. Evol Bioinform Online (2015) 0.76
Observation selection bias in contact prediction and its implications for structural bioinformatics. Sci Rep (2016) 0.75
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Sparse inverse covariance estimation with the graphical lasso. Biostatistics (2007) 24.38
Macromolecular modeling with rosetta. Annu Rev Biochem (2008) 8.32
Correlated mutations and residue contacts in proteins. Proteins (1994) 5.20
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics (2011) 3.89
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics (2007) 3.42
Disulfide bonds and protein folding. Biochemistry (2000) 2.03
Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol (2010) 1.98
Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des (1997) 1.78
Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics (2004) 1.58
Predicting disulfide bond connectivity in proteins by correlated mutations analysis. Bioinformatics (2008) 1.57
Prediction of disulfide connectivity in proteins. Bioinformatics (2001) 1.44
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins (2006) 1.41
Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics (2005) 1.38
Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins (2001) 1.36
Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins (2002) 1.35
Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins (2004) 1.19
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinformatics (2007) 1.14
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng (2002) 1.09
Structural basis of protein disulfide bond generation in the cell. Genes Cells (2010) 0.99
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinformatics (2011) 0.94
Analysis of superfamily specific profile-profile recognition accuracy. BMC Bioinformatics (2004) 0.93
A simplified approach to disulfide connectivity prediction from protein sequences. BMC Bioinformatics (2008) 0.86
Is there an optimal substitution matrix for contact prediction with correlated mutations? IEEE/ACM Trans Comput Biol Bioinform (2011) 0.79
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol Biol (2009) 0.78
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
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
Transglutaminases: nature's biological glues. Biochem J (2002) 3.42
Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat (2009) 3.14
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics (2003) 3.10
Prediction of coordination number and relative solvent accessibility in proteins. Proteins (2002) 2.66
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
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
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
CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype. Blood (2013) 1.28
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
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
Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. Hum Mutat (2008) 1.11
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
New Escherichia coli outer membrane proteins identified through prediction and experimental verification. Protein Sci (2006) 1.00
Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J Mol Biol (2005) 1.00
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res (2011) 0.99
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res (2010) 0.99
Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the herpes simplex virus gD binding site confers high-affinity binding to gD. J Virol (2002) 0.98
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
Hierarchical mechanochemical switches in angiostatin. Chembiochem (2006) 0.90
Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics (2008) 0.89
Expression of IGF-1 receptor in KIT/PDGF receptor-α wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction. Future Oncol (2013) 0.88
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
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics (2012) 0.87