Published in J Mol Biol on January 09, 2004
Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. Biochem J (2005) 2.79
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
Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer. Mol Cell (2008) 1.46
Aromatic-proline interactions: electronically tunable CH/π interactions. Acc Chem Res (2012) 1.01
Role of the C-terminal SH3 domain and N-terminal tyrosine phosphorylation in regulation of Tim and related Dbl-family proteins. Biochemistry (2008) 0.96
o-Nitrotyrosine and p-iodophenylalanine as spectroscopic probes for structural characterization of SH3 complexes. Protein Sci (2007) 0.80
Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex. PLoS Comput Biol (2011) 0.80
New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae. Protein Sci (2006) 0.80
Evolution of the SH3 Domain Specificity Landscape in Yeasts. PLoS One (2015) 0.76
Arginine mimetics using α-guanidino acids: introduction of functional groups and stereochemistry adjacent to recognition guanidiniums in peptides. Chembiochem (2011) 0.75
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
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
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
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
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
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
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
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
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
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
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
Design of a wearable device for ECG continuous monitoring using wireless technology. Conf Proc IEEE Eng Med Biol Soc (2004) 1.28
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Space as the final frontier in stochastic simulations of biological systems. FEBS Lett (2005) 1.25
Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet (2007) 1.24
Engineering signal transduction pathways. Cell (2010) 1.21
Computational design of peptide ligands. Trends Biotechnol (2011) 1.19
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res (2010) 1.19
Unspecific hydrophobic stabilization of folding transition states. Proc Natl Acad Sci U S A (2002) 1.16
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res (2010) 1.16
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15
Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol (2006) 1.15
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol (2005) 1.15
Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics (2012) 1.15
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014. Am J Respir Crit Care Med (2015) 1.12
Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Sci Signal (2009) 1.12
Structures in systems biology. Curr Opin Struct Biol (2007) 1.11
Analysis of disease-linked rhodopsin mutations based on structure, function, and protein stability calculations. J Mol Biol (2010) 1.10
Human epidermal stem cell function is regulated by circadian oscillations. Cell Stem Cell (2013) 1.09
The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol (2005) 1.08
Localized transfection on arrays of magnetic beads coated with PCR products. Nat Methods (2005) 1.06
Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat Struct Biol (2002) 1.06
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC Struct Biol (2008) 1.05
Transcription start site associated RNAs in bacteria. Mol Syst Biol (2012) 1.04
Strategies for protein synthetic biology. Nucleic Acids Res (2010) 1.04
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol (2005) 1.04
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
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol (2008) 1.02
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci U S A (2008) 1.01
High frequency of germline succinate dehydrogenase mutations in sporadic cervical paragangliomas in northern Spain: mitochondrial succinate dehydrogenase structure-function relationships and clinical-pathological correlations. J Clin Endocrinol Metab (2007) 1.01
DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design. J Biol Chem (2008) 1.01
Insights into the origin of the tendency of the PI3-SH3 domain to form amyloid fibrils. J Mol Biol (2002) 1.00
BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res (2010) 0.98
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol Syst Biol (2011) 0.95
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol Syst Biol (2013) 0.95
Amyloid toxicity is independent of polypeptide sequence, length and chirality. J Mol Biol (2007) 0.95
Synthetic biology: challenges ahead. Bioinformatics (2006) 0.95
Combinatorial approaches: a new tool to search for highly structured beta-hairpin peptides. Proc Natl Acad Sci U S A (2002) 0.95
Building blocks for protein interaction devices. Nucleic Acids Res (2010) 0.94
Integration of protein abundance and structure data reveals competition in the ErbB signaling network. Sci Signal (2013) 0.94
A genome-wide Ras-effector interaction network. J Mol Biol (2007) 0.94
A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core. J Mol Biol (2003) 0.94
In situ overlap and sequence synthesis during DNA assembly. ACS Synth Biol (2013) 0.93
Hacking the code of amyloid formation: the amyloid stretch hypothesis. Prion (2007) 0.93
Engineering of weak helper interactions for high-efficiency FRET probes. Nat Methods (2013) 0.92
E-cadherin destabilization accounts for the pathogenicity of missense mutations in hereditary diffuse gastric cancer. PLoS One (2012) 0.91
Protein-peptide complex prediction through fragment interaction patterns. Structure (2013) 0.91
Interaction of the human somatostatin receptor 3 with the multiple PDZ domain protein MUPP1 enables somatostatin to control permeability of epithelial tight junctions. FEBS Lett (2008) 0.91
Fractionation of organosolv lignin from olive tree clippings and its valorization to simple phenolic compounds. ChemSusChem (2013) 0.90
Enhancement of antitumor properties of rhTRAIL by affinity increase toward its death receptors. Biochemistry (2009) 0.90