Published in J Chem Inf Model on October 01, 2008
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One (2011) 1.28
The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol (2010) 1.12
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res (2011) 1.06
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Comput Biol (2010) 1.02
Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. PLoS One (2012) 0.89
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics (2013) 0.86
Fast and accurate discovery of degenerate linear motifs in protein sequences. PLoS One (2014) 0.82
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. Nucleic Acids Res (2015) 0.77
Facile iterative synthesis of 2,5-terpyrimidinylenes as nonpeptidic alpha-helical mimics. J Org Chem (2010) 0.75
The Functional Human C-Terminome. PLoS One (2016) 0.75
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS One (2007) 2.55
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet (2012) 2.53
Potential artefacts in protein-interaction networks. FEBS Lett (2002) 2.24
3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res (2005) 2.18
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet (2010) 2.15
Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci (2010) 2.06
Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Am J Hum Genet (2009) 2.04
A structural perspective on protein-protein interactions. Curr Opin Struct Biol (2004) 1.98
Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. Am J Hum Genet (2012) 1.96
Interactome3D: adding structural details to protein networks. Nat Methods (2012) 1.89
A network medicine approach to human disease. FEBS Lett (2009) 1.83
CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics (2008) 1.82
Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72
Bioinformatic discovery of novel bioactive peptides. Nat Chem Biol (2007) 1.72
3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2010) 1.71
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res (2006) 1.61
3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res (2008) 1.51
Blood pressure loci identified with a gene-centric array. Am J Hum Genet (2011) 1.44
A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet (2011) 1.43
Contextual specificity in peptide-mediated protein interactions. PLoS One (2008) 1.37
Structural insights into the target specificity of plant invertase and pectin methylesterase inhibitory proteins. Plant Cell (2004) 1.33
Targeting and tinkering with interaction networks. Nat Chem Biol (2008) 1.27
Ribonucleotide reductases: divergent evolution of an ancient enzyme. J Mol Evol (2002) 1.26
SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res (2011) 1.23
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol (2009) 1.22
Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr Opin Struct Biol (2011) 1.21
Towards a detailed atlas of protein-protein interactions. Curr Opin Struct Biol (2013) 1.19
Structures of YAP protein domains reveal promising targets for development of new cancer drugs. Semin Cell Dev Biol (2012) 1.19
Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics (2003) 1.17
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics (2009) 1.17
Genome-wide association study of genetic determinants of LDL-c response to atorvastatin therapy: importance of Lp(a). J Lipid Res (2012) 1.17
Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol (2005) 1.16
The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res (2007) 1.16
Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Mol Biol Evol (2003) 1.16
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput (2015) 1.15
3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2013) 1.14
Prediction of short linear protein binding regions. J Mol Biol (2011) 1.14
Dynamic interactions of proteins in complex networks: a more structured view. FEBS J (2009) 1.13
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A (2012) 1.13
Human tissue profiling with multidimensional protein identification technology. J Proteome Res (2005) 1.07
SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res (2012) 1.04
Interactome-wide prediction of short, disordered protein interaction motifs in humans. Mol Biosyst (2011) 1.03
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome Res (2010) 1.02
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res (2010) 1.02
Cattle demographic history modelled from autosomal sequence variation. Philos Trans R Soc Lond B Biol Sci (2010) 1.02
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Comput Biol (2010) 1.02
Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evol Dev (2004) 1.01
GASP: Gapped Ancestral Sequence Prediction for proteins. BMC Bioinformatics (2004) 1.01
Analysis of chemical and biological features yields mechanistic insights into drug side effects. Chem Biol (2013) 1.00
A genome-wide association study of recipient genotype and medium-term kidney allograft function. Clin Transplant (2013) 1.00
Uncovering new substrates for Aurora A kinase. EMBO Rep (2010) 1.00
Computational identification and analysis of protein short linear motifs. Front Biosci (Landmark Ed) (2010) 1.00
Recycling side-effects into clinical markers for drug repositioning. Genome Med (2012) 0.99
Towards a molecular characterisation of pathological pathways. FEBS Lett (2008) 0.96
Insider access: pepducin symposium explores a new approach to GPCR modulation. Ann N Y Acad Sci (2009) 0.96
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinformatics (2010) 0.95
The role of structural disorder in the rewiring of protein interactions through evolution. Mol Cell Proteomics (2012) 0.95
Predicting the important enzymes in human breast milk digestion. J Agric Food Chem (2014) 0.92
The proton-pump inhibitor lansoprazole enhances amyloid beta production. PLoS One (2013) 0.91
BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinformatics (2005) 0.91
Optimal stepwise experimental design for pairwise functional interaction studies. Bioinformatics (2008) 0.90
Target selection for complex structural genomics. Curr Opin Struct Biol (2006) 0.90
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. Nucleic Acids Res (2012) 0.90
A novel framework for the comparative analysis of biological networks. PLoS One (2012) 0.89
Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. PLoS One (2012) 0.89
Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians. BMC Med Genet (2005) 0.88
Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression. J Virol (2010) 0.88
Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. PLoS One (2013) 0.87
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions. BMC Syst Biol (2009) 0.86
A second-generation protein-protein interaction network of Helicobacter pylori. Mol Cell Proteomics (2014) 0.86
EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. J Proteome Res (2012) 0.85
Tools for the identification of variable and potentially variable tandem repeats. BMC Genomics (2006) 0.84
Marked variability in the extent of protein disorder within and between viral families. PLoS One (2013) 0.84
Profile-based short linear protein motif discovery. BMC Bioinformatics (2012) 0.83
Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution. Proteins (2011) 0.83
Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins. PLoS One (2012) 0.83
Peptide-binding domains: are limp handshakes safest? Sci Signal (2012) 0.83
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure (2011) 0.83
Functional and structural analysis of C-terminal BRCA1 missense variants. PLoS One (2013) 0.82
Platelet glycoprotein Ib alpha receptor polymorphisms and recurrent ischaemic events in acute coronary syndrome patients. J Thromb Thrombolysis (2002) 0.82
Following the digestion of milk proteins from mother to baby. J Proteome Res (2014) 0.82
From protein interaction networks to novel therapeutic strategies. IUBMB Life (2012) 0.82
Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits. Proteomics (2008) 0.82
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations. Structure (2010) 0.82
Genetic stratification of pathogen-response-related and other variants within a homogeneous Caucasian Irish population. Eur J Hum Genet (2005) 0.82
Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization. J Chem Inf Model (2009) 0.81
The impact of genetic variation in the region of the GPIIIa gene, on Pl expression bias and GPIIb/IIIa receptor density in platelets. Br J Haematol (2006) 0.81
Ligand switching in cell-permeable peptides: manipulation of the alpha-integrin signature motif. ACS Chem Biol (2009) 0.81
CPPpred: prediction of cell penetrating peptides. Bioinformatics (2013) 0.81
Uroplakin III is not a major candidate gene for primary vesicoureteral reflux. Eur J Hum Genet (2005) 0.81
Structural systems pharmacology: the role of 3D structures in next-generation drug development. Chem Biol (2013) 0.81
CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids. J Chem Inf Model (2011) 0.81
Elevated white cell count in acute coronary syndromes: relationship to variants in inflammatory and thrombotic genes. BMC Med Genet (2004) 0.81
Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication. Mol Biol Evol (2006) 0.80
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. Protein Sci (2011) 0.80
Molecular evolution of CXC chemokines and receptors. Trends Immunol (2003) 0.80