Published in Nucleic Acids Res on October 30, 2009
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56
Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions. Nucleic Acids Res (2011) 1.85
3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2010) 1.71
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res (2012) 1.71
Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One (2011) 1.28
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21
3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2013) 1.14
Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins (2010) 1.11
A unified conformational selection and induced fit approach to protein-peptide docking. PLoS One (2013) 1.10
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res (2011) 1.06
Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol (2011) 1.04
BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res (2010) 0.98
In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. Biochemistry (2012) 0.96
Mining tertiary structural motifs for assessment of designability. Methods Enzymol (2013) 0.87
Learning a peptide-protein binding affinity predictor with kernel ridge regression. BMC Bioinformatics (2013) 0.87
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics (2013) 0.86
Bimolecular integrin-ligand interactions quantified using peptide-functionalized dextran-coated microparticles. Integr Biol (Camb) (2011) 0.83
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. Genome Med (2014) 0.82
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. Database (Oxford) (2014) 0.80
DOMMINO: a database of macromolecular interactions. Nucleic Acids Res (2011) 0.80
Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput Biol (2015) 0.79
Break CDK2/Cyclin E1 interface allosterically with small peptides. PLoS One (2014) 0.77
Secondary structure, a missing component of sequence-based minimotif definitions. PLoS One (2012) 0.77
A Comprehensive View of the β-Arrestinome. Front Endocrinol (Lausanne) (2017) 0.75
PepComposer: computational design of peptides binding to a given protein surface. Nucleic Acids Res (2016) 0.75
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. Database (Oxford) (2016) 0.75
A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets. J Cheminform (2015) 0.75
PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun (2014) 0.75
Protein structural motifs in prediction and design. Curr Opin Struct Biol (2017) 0.75
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74
The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res (2008) 14.82
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Assembly of cell regulatory systems through protein interaction domains. Science (2003) 10.59
The PROSITE database. Nucleic Acids Res (2006) 8.11
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
MUSTANG: a multiple structural alignment algorithm. Proteins (2006) 4.69
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res (2008) 2.92
Computational design of peptides that target transmembrane helices. Science (2007) 2.28
PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Peptides mediating interaction networks: new leads at last. Curr Opin Biotechnol (2006) 1.75
DOMINE: a database of protein domain interactions. Nucleic Acids Res (2007) 1.54
3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res (2008) 1.51
FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Res (2006) 1.45
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics (2005) 1.42
Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol (2008) 1.39
3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res (2007) 1.27
Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature (1994) 1.26
PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res (2007) 1.18
Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PLoS Comput Biol (2008) 1.04
Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. Structure (2009) 1.04
MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Appl Bioinformatics (2006) 1.02
Approved drug mimics of short peptide ligands from protein interaction motifs. J Chem Inf Model (2008) 0.98
Semirational design of a potent, artificial agonist of fibroblast growth factor receptors. Nat Biotechnol (1999) 0.92
Hmrbase: a database of hormones and their receptors. BMC Genomics (2009) 0.88
Protein design in biological networks: from manipulating the input to modifying the output. Protein Eng Des Sel (2009) 0.87
The complex route to MHC class I-peptide complexes. Cell (2006) 0.80
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res (2006) 3.04
Gain of function of mutant p53 by coaggregation with multiple tumor suppressors. Nat Chem Biol (2011) 2.94
VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials. Lancet Oncol (2012) 2.92
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
From in vivo to in silico biology and back. Nature (2006) 2.74
The mechanism of γ-Secretase dysfunction in familial Alzheimer disease. EMBO J (2012) 2.72
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol (2006) 2.69
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Lipids revert inert Abeta amyloid fibrils to neurotoxic protofibrils that affect learning in mice. EMBO J (2007) 2.39
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
Neurotoxicity of Alzheimer's disease Aβ peptides is induced by small changes in the Aβ42 to Aβ40 ratio. EMBO J (2010) 2.26
The stability effects of protein mutations appear to be universally distributed. J Mol Biol (2007) 2.25
Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol (2004) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Analysis and description of HOLTIN service provision for AECG monitoring in complex indoor environments. Sensors (Basel) (2013) 2.02
Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol Cell Proteomics (2008) 2.01
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol (2005) 1.91
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci U S A (2004) 1.83
Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76
Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics (2006) 1.69
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58
Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control study. Breast Cancer Res (2010) 1.51
A graphical interface for the FoldX forcefield. Bioinformatics (2011) 1.50
Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol (2005) 1.48
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res (2011) 1.44
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res (2007) 1.43
A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
Redox proteomics of protein-bound methionine oxidation. Mol Cell Proteomics (2011) 1.37
Towards cellular systems in 4D. Cell (2005) 1.33
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
Analyzing protein interaction networks using structural information. Annu Rev Biochem (2008) 1.32
Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease. Hum Mutat (2008) 1.31
Design of a wearable device for ECG continuous monitoring using wireless technology. Conf Proc IEEE Eng Med Biol Soc (2004) 1.28