Published in Protein Eng Des Sel on June 26, 2009
Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins (2010) 2.56
SDM--a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res (2011) 2.28
Deep mutational scanning: a new style of protein science. Nat Methods (2014) 2.05
Phosphorylation in protein-protein binding: effect on stability and function. Structure (2011) 1.96
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics (2011) 1.76
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. BMC Genomics (2012) 1.62
Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol (2013) 1.59
The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat Rev Genet (2010) 1.58
Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol (2010) 1.47
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc Natl Acad Sci U S A (2012) 1.39
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Inferring causality and functional significance of human coding DNA variants. Hum Mol Genet (2012) 1.31
Molecular mechanisms of disease-causing missense mutations. J Mol Biol (2013) 1.31
Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci U S A (2013) 1.28
Towards precision medicine: advances in computational approaches for the analysis of human variants. J Mol Biol (2013) 1.23
An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol (2014) 1.19
A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol (2014) 1.19
RosettaBackrub--a web server for flexible backbone protein structure modeling and design. Nucleic Acids Res (2010) 1.16
Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. Proc Natl Acad Sci U S A (2010) 1.04
Predicting changes in protein thermostability brought about by single- or multi-site mutations. BMC Bioinformatics (2010) 0.99
Assessing predictors of changes in protein stability upon mutation using self-consistency. PLoS One (2012) 0.96
Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs. Mol Biol Evol (2015) 0.95
Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl (2013) 0.95
Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods. Protein Sci (2012) 0.93
High-throughput measurement, correlation analysis, and machine-learning predictions for pH and thermal stabilities of Pfizer-generated antibodies. Protein Sci (2011) 0.93
First-step mutations for adaptation at elevated temperature increase capsid stability in a virus. PLoS One (2011) 0.93
Contingency and entrenchment in protein evolution under purifying selection. Proc Natl Acad Sci U S A (2015) 0.92
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol (2014) 0.92
Tradeoff between stability and multispecificity in the design of promiscuous proteins. PLoS Comput Biol (2009) 0.92
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Phys Biol (2015) 0.92
Impact of mutations on the allosteric conformational equilibrium. J Mol Biol (2012) 0.91
Conformational diversity and computational enzyme design. Curr Opin Chem Biol (2010) 0.91
Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PLoS One (2014) 0.90
Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PLoS Comput Biol (2012) 0.90
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. Bioinformatics (2011) 0.89
Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. Hum Mutat (2012) 0.89
Targeted modification of wheat grain protein to reduce the content of celiac causing epitopes. Funct Integr Genomics (2012) 0.88
Structure-based redesign of the binding specificity of anti-apoptotic Bcl-x(L). J Mol Biol (2012) 0.88
Frontier of therapeutic antibody discovery: The challenges and how to face them. World J Biol Chem (2012) 0.88
Personalized biochemistry and biophysics. Biochemistry (2015) 0.88
Epistasis in protein evolution. Protein Sci (2016) 0.88
How structural and physicochemical determinants shape sequence constraints in a functional enzyme. PLoS One (2015) 0.88
Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J Am Chem Soc (2014) 0.87
A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Comput Biol (2012) 0.87
The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. Mol Cancer (2011) 0.87
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci (2014) 0.86
PROTS: a fragment based protein thermo-stability potential. Proteins (2011) 0.86
Kinetic and structural characterization of thermostabilized mutants of human carbonic anhydrase II. Protein Eng Des Sel (2012) 0.85
Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality. PLoS Genet (2015) 0.85
Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Hum Mutat (2012) 0.85
Protein thermostability prediction within homologous families using temperature-dependent statistical potentials. PLoS One (2014) 0.84
The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease. J Mol Biol (2015) 0.84
Protein stability: computation, sequence statistics, and new experimental methods. Curr Opin Struct Biol (2015) 0.83
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. BMC Bioinformatics (2010) 0.83
The contribution of coevolving residues to the stability of KDO8P synthase. PLoS One (2011) 0.82
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One (2015) 0.82
Computational approaches to study the effects of small genomic variations. J Mol Model (2015) 0.81
Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. PLoS Comput Biol (2015) 0.81
PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One (2012) 0.81
Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PLoS One (2012) 0.81
Structural and catalytic effects of proline substitution and surface loop deletion in the extended active site of human carbonic anhydrase II. FEBS J (2015) 0.81
Engineering a more thermostable blue light photo receptor Bacillus subtilis YtvA LOV domain by a computer aided rational design method. PLoS Comput Biol (2013) 0.81
Determinants for the improved thermostability of a mesophilic family 11 xylanase predicted by computational methods. Biotechnol Biofuels (2014) 0.81
MAESTRO - multi agent stability prediction upon point mutations. BMC Bioinformatics (2015) 0.80
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol Cell (2016) 0.80
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. J Mol Biol (2014) 0.80
Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions. PLoS One (2014) 0.80
Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol (2016) 0.79
The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins (2011) 0.79
Grading amino acid properties increased accuracies of single point mutation on protein stability prediction. BMC Bioinformatics (2012) 0.79
Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci (2012) 0.78
Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. J Mol Model (2010) 0.78
Identification and glycerol-induced correction of misfolding mutations in the X-linked mental retardation gene CASK. PLoS One (2014) 0.78
A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel (2016) 0.78
PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat (2017) 0.78
Computational approaches for predicting mutant protein stability. J Comput Aided Mol Des (2016) 0.78
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. Genetics (2016) 0.77
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. PLoS Comput Biol (2016) 0.77
Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life. PLoS One (2016) 0.77
A rational free energy-based approach to understanding and targeting disease-causing missense mutations. J Am Med Inform Assoc (2013) 0.77
Contribution of inter-subunit interactions to the thermostability of Pyrococcus furiosus citrate synthase. Extremophiles (2011) 0.76
Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A. J Mol Model (2014) 0.76
Principal component analysis of binding energies for single-point mutants of hT2R16 bound to an agonist correlate with experimental mutant cell response. J Comput Biol (2015) 0.76
Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools. PLoS One (2015) 0.76
Impact of the 237th residue on the folding of human carbonic anhydrase II. Int J Mol Sci (2011) 0.76
High-throughput identification of protein mutant stability computed from a double mutant fitness landscape. Protein Sci (2015) 0.75
Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface. J Biol Chem (2015) 0.75
Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists. J Comput Aided Mol Des (2012) 0.75
Prediction of protein relative enthalpic stability from molecular dynamics simulations of the folded and unfolded states. Biophys J (2012) 0.75
Directed evolution of the substrate specificity of dialkylglycine decarboxylase. Biochim Biophys Acta (2014) 0.75
Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1. Biophys J (2016) 0.75
Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis. MBio (2016) 0.75
Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine. Curr Opin Struct Biol (2015) 0.75
Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches. PLoS Comput Biol (2016) 0.75
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. Methods Mol Biol (2017) 0.75
Thermostability of Enzymes from Molecular Dynamics Simulations. J Chem Theory Comput (2016) 0.75
Computational tools help improve protein stability but with a solubility tradeoff. J Biol Chem (2017) 0.75
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. J Comput Aided Mol Des (2012) 0.75
ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol (2004) 3.18
Structural linkage between ligand discrimination and receptor activation by type I interferons. Cell (2011) 2.39
Two-state folding observed in individual protein molecules. J Am Chem Soc (2004) 2.14
Inquiring into the differential action of interferons (IFNs): an IFN-alpha2 mutant with enhanced affinity to IFNAR1 is functionally similar to IFN-beta. Mol Cell Biol (2006) 1.82
Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions. Methods (2012) 1.75
The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol (2007) 1.59
Protein-protein association in polymer solutions: from dilute to semidilute to concentrated. Biophys J (2006) 1.40
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Separating the contribution of translational and rotational diffusion to protein association. J Am Chem Soc (2005) 1.39
Structural and dynamic determinants of type I interferon receptor assembly and their functional interpretation. Immunol Rev (2012) 1.38
Effect of crowding on protein-protein association rates: fundamental differences between low and high mass crowding agents. J Mol Biol (2004) 1.34
Common crowding agents have only a small effect on protein-protein interactions. Biophys J (2009) 1.33
The stability of the ternary interferon-receptor complex rather than the affinity to the individual subunits dictates differential biological activities. J Biol Chem (2008) 1.33
eMovie: a storyboard-based tool for making molecular movies. Trends Biochem Sci (2007) 1.29
Stochastic receptor expression determines cell fate upon interferon treatment. Mol Cell Biol (2011) 1.26
Mutational analysis of the IFNAR1 binding site on IFNalpha2 reveals the architecture of a weak ligand-receptor binding-site. J Mol Biol (2005) 1.25
Binding and activity of all human alpha interferon subtypes. Cytokine (2011) 1.24
Receptor density is key to the alpha2/beta interferon differential activities. Mol Cell Biol (2009) 1.22
An interferon alpha2 mutant optimized by phage display for IFNAR1 binding confers specifically enhanced antitumor activities. J Biol Chem (2007) 1.21
The fast release of sticky protons: kinetics of substrate binding and proton release in a multidrug transporter. Proc Natl Acad Sci U S A (2007) 1.20
On the contribution of water-mediated interactions to protein-complex stability. Biochemistry (2007) 1.19
Exploring the charge space of protein-protein association: a proteomic study. Proteins (2005) 1.14
Fruitful and futile encounters along the association reaction between proteins. Biophys J (2009) 1.08
Upregulation of a small subset of genes drives type I interferon-induced antiviral memory. J Interferon Cytokine Res (2007) 1.05
On the dynamic nature of the transition state for protein-protein association as determined by double-mutant cycle analysis and simulation. J Mol Biol (2007) 1.01
Variations in the unstructured C-terminal tail of interferons contribute to differential receptor binding and biological activity. J Mol Biol (2006) 1.00
The human type I interferon receptor: NMR structure reveals the molecular basis of ligand binding. Structure (2003) 0.98
Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci U S A (2012) 0.97
Noncovalent, site-specific biotinylation of histidine-tagged proteins. Anal Chem (2007) 0.96
Formation of protein complexes in crowded environments--from in vitro to in vivo. FEBS Lett (2013) 0.94
Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys J (2012) 0.93
Mutation of the IFNAR-1 receptor binding site of human IFN-alpha2 generates type I IFN competitive antagonists. Biochemistry (2008) 0.91
Understanding hydrogen-bond patterns in proteins using network motifs. Bioinformatics (2009) 0.91
Docking of antizyme to ornithine decarboxylase and antizyme inhibitor using experimental mutant and double-mutant cycle data. J Mol Biol (2009) 0.90
Similar chemistry, but different bond preferences in inter versus intra-protein interactions. Proteins (2008) 0.90
Reversible PEGylation: a novel technology to release native interferon alpha2 over a prolonged time period. J Med Chem (2004) 0.90
The human interferon receptor: NMR-based modeling, mapping of the IFN-alpha 2 binding site, and observed ligand-induced tightening. Biochemistry (2002) 0.90
Binding Characteristics of IFN-alpha Subvariants to IFNAR2-EC and Influence of the 6-Histidine Tag. J Interferon Cytokine Res (2006) 0.88
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng Des Sel (2004) 0.87
Optimizing the binding affinity of a carrier protein: a case study on the interaction between soluble ifnar2 and interferon beta. J Biol Chem (2004) 0.87
Four distances between pairs of amino acids provide a precise description of their interaction. PLoS Comput Biol (2009) 0.86
Cluster conservation as a novel tool for studying protein-protein interactions evolution. Proteins (2008) 0.86
Type I interferons induce apoptosis by balancing cFLIP and caspase-8 independent of death ligands. Mol Cell Biol (2012) 0.84
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. BMC Bioinformatics (2010) 0.83
Improved binding of raf to Ras.GDP is correlated with biological activity. J Biol Chem (2009) 0.83
PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins. J Chem Inf Model (2014) 0.82
A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces. Chemistry (2010) 0.80
Three-dimensional structure determination of proteins related to human health in their functional context at The Israel Structural Proteomics Center (ISPC). This paper was presented at ICCBM10. Acta Crystallogr D Biol Crystallogr (2005) 0.80
Protein-surface interactions: challenging experiments and computations. J Mol Recognit (2010) 0.79
ProMateus--an open research approach to protein-binding sites analysis. Nucleic Acids Res (2007) 0.78
Rediscovering secondary structures as network motifs--an unsupervised learning approach. Bioinformatics (2007) 0.78
FRETex: a FRET-based, high-throughput technique to analyze protein-protein interactions. Protein Eng Des Sel (2012) 0.77
The nitty-gritty of protein interactions. Structure (2005) 0.76
"4D Biology for health and disease" workshop report. N Biotechnol (2010) 0.75