Published in Nucleic Acids Res on July 01, 2005
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res (2006) 3.04
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature (2009) 2.61
Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3. Proc Natl Acad Sci U S A (2009) 2.55
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat Genet (2015) 2.34
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
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
Widespread macromolecular interaction perturbations in human genetic disorders. Cell (2015) 2.11
Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucleic Acids Res (2010) 1.92
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
Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol (2009) 1.54
Bioinformatics for personal genome interpretation. Brief Bioinform (2012) 1.51
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. Am J Hum Genet (2013) 1.46
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res (2011) 1.44
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Cell (2017) 1.38
Functional significance of rare neuroligin 1 variants found in autism. PLoS Genet (2017) 1.38
Contextual specificity in peptide-mediated protein interactions. PLoS One (2008) 1.37
Redox proteomics of protein-bound methionine oxidation. Mol Cell Proteomics (2011) 1.37
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Computational analysis of missense mutations causing Snyder-Robinson syndrome. Hum Mutat (2010) 1.31
Analysis and functional prediction of reactive cysteine residues. J Biol Chem (2011) 1.29
Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci U S A (2013) 1.28
Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity. Mol Cell Proteomics (2009) 1.27
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
Towards precision medicine: advances in computational approaches for the analysis of human variants. J Mol Biol (2013) 1.23
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Genome Med (2012) 1.21
RosettaBackrub--a web server for flexible backbone protein structure modeling and design. 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
The functional effect of pathogenic mutations in Rab escort protein 1. Mutat Res (2009) 1.15
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One (2009) 1.14
Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type. Am J Hum Genet (2011) 1.13
Chemical chaperones assist intracellular folding to buffer mutational variations. Nat Chem Biol (2012) 1.12
Predicting folding free energy changes upon single point mutations. Bioinformatics (2012) 1.12
Computational prediction of protein hot spot residues. Curr Pharm Des (2012) 1.11
Molecular modeling of the full-length human TRPV1 channel in closed and desensitized states. J Membr Biol (2008) 1.11
Mutations in RIPK4 cause the autosomal-recessive form of popliteal pterygium syndrome. Am J Hum Genet (2011) 1.11
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res (2010) 1.10
Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis. Plant Cell (2014) 1.09
Shifting transition states in the unfolding of a large ankyrin repeat protein. Proc Natl Acad Sci U S A (2008) 1.08
Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing. J Mol Biol (2012) 1.06
Angiopoietin receptor TEK mutations underlie primary congenital glaucoma with variable expressivity. J Clin Invest (2016) 1.05
Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res (2012) 1.05
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC Struct Biol (2008) 1.05
Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med (2012) 1.04
RANKL employs distinct binding modes to engage RANK and the osteoprotegerin decoy receptor. Structure (2012) 1.04
Stability of domain structures in multi-domain proteins. Sci Rep (2011) 1.03
Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. J Mol Biol (2012) 1.03
Comparative analysis of species-specific ligand recognition in Toll-like receptor 8 signaling: a hypothesis. PLoS One (2011) 1.02
Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PLoS Genet (2011) 1.02
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics (2007) 1.02
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol (2008) 1.02
α-Galactosidase aggregation is a determinant of pharmacological chaperone efficacy on Fabry disease mutants. J Biol Chem (2012) 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
Increased monomerization of mutant HSPB1 leads to protein hyperactivity in Charcot-Marie-Tooth neuropathy. J Biol Chem (2010) 1.01
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
Accurate prediction of DnaK-peptide binding via homology modelling and experimental data. PLoS Comput Biol (2009) 1.01
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures. Nucleic Acids Res (2015) 1.00
Molecular modeling of retinoschisin with functional analysis of pathogenic mutations from human X-linked retinoschisis. Hum Mol Genet (2010) 1.00
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics (2012) 1.00
Structure of the dimerization domain of the rabies virus phosphoprotein. J Virol (2010) 1.00
Predicting changes in protein thermostability brought about by single- or multi-site mutations. BMC Bioinformatics (2010) 0.99
Structural insight into unique cardiac myosin-binding protein-C motif: a partially folded domain. J Biol Chem (2012) 0.98
BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res (2010) 0.98
Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci (2014) 0.97
Structure-based analysis of five novel disease-causing mutations in 21-hydroxylase-deficient patients. PLoS One (2011) 0.95
Structural consensus among antibodies defines the antigen binding site. PLoS Comput Biol (2012) 0.94
On human disease-causing amino acid variants: statistical study of sequence and structural patterns. Hum Mutat (2015) 0.93
Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins. Biophys J (2007) 0.93
Stability-activity tradeoffs constrain the adaptive evolution of RubisCO. Proc Natl Acad Sci U S A (2014) 0.92
ATP1A3 mutations and genotype-phenotype correlation of alternating hemiplegia of childhood in Chinese patients. PLoS One (2014) 0.92
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PLoS Comput Biol (2011) 0.92
Interaction patches of procaspase-1 caspase recruitment domains (CARDs) are differently involved in procaspase-1 activation and receptor-interacting protein 2 (RIP2)-dependent nuclear factor κB signaling. J Biol Chem (2011) 0.92
On the importance of polar interactions for complexes containing intrinsically disordered proteins. PLoS Comput Biol (2013) 0.92
Engineering of weak helper interactions for high-efficiency FRET probes. Nat Methods (2013) 0.92
Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors. PLoS One (2015) 0.92
E-cadherin destabilization accounts for the pathogenicity of missense mutations in hereditary diffuse gastric cancer. PLoS One (2012) 0.91
In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Sci Rep (2016) 0.91
Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. Proc Natl Acad Sci U S A (2013) 0.91
DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Commun Comput Phys (2013) 0.91
The conserved His-144 in the PsbP protein is important for the interaction between the PsbP N-terminus and the Cyt b559 subunit of photosystem II. J Biol Chem (2012) 0.90
Roles of residues in the interface of transient protein-protein complexes before complexation. Sci Rep (2012) 0.90
FOXC2 mutations in familial and sporadic spinal extradural arachnoid cyst. PLoS One (2013) 0.90
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform (2014) 0.90
Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. Biophys J (2009) 0.89
Structural basis of Rnd1 binding to plexin Rho GTPase binding domains (RBDs). J Biol Chem (2011) 0.89
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. BMC Bioinformatics (2009) 0.89
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLoS Comput Biol (2015) 0.89
Hyaluronan modulates TRPV1 channel opening, reducing peripheral nociceptor activity and pain. Nat Commun (2015) 0.89
Positively selected sites in cetacean myoglobins contribute to protein stability. PLoS Comput Biol (2013) 0.89
Redox biology: computational approaches to the investigation of functional cysteine residues. Antioxid Redox Signal (2011) 0.89
Mutations in extracellular matrix genes NID1 and LAMC1 cause autosomal dominant Dandy-Walker malformation and occipital cephaloceles. Hum Mutat (2013) 0.88
Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity. Oncogene (2015) 0.88
The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics (2012) 0.88
Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning. PLoS Comput Biol (2014) 0.88
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis (1997) 57.27
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
WHAT IF: a molecular modeling and drug design program. J Mol Graph (1990) 24.35
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41
Rational design of faster associating and tighter binding protein complexes. Nat Struct Biol (2000) 3.03
Molecular basis for amyloid fibril formation and stability. Proc Natl Acad Sci U S A (2005) 3.00
Effective energy functions for protein structure prediction. Curr Opin Struct Biol (2000) 2.92
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Evaluation of protein models by atomic solvation preference. J Mol Biol (1992) 2.53
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci (1996) 2.46
Getting out of shape. Nature (2002) 1.71
The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol (2000) 1.45
Dependence of formation of small disulfide loops in two-cysteine peptides on the number and types of intervening amino acids. J Biol Chem (1989) 1.44
A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42
Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39
Local water bridges and protein conformational stability. Protein Sci (1999) 1.32
Excluded volume approximation to protein-solvent interaction. The solvent contact model. Biophys J (1990) 1.30
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Disulfide bonds in protein folding and stability. Methods Mol Biol (1995) 1.20
Protein design based on folding models. Curr Opin Struct Biol (2001) 1.11
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
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
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
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
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
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
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity. Mol Cell Proteomics (2009) 1.27
Structural basis for increased toxicity of pathological aβ42:aβ40 ratios in Alzheimer disease. J Biol Chem (2011) 1.26
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
Mutations other than null mutations producing a pathogenic loss of progranulin in frontotemporal dementia. Hum Mutat (2007) 1.20
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res (2010) 1.19
Computational design of peptide ligands. Trends Biotechnol (2011) 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
The culprit behind amyloid beta peptide related neurotoxicity in Alzheimer's disease: oligomer size or conformation? Alzheimers Res Ther (2010) 1.09
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