Published in J Mol Biol on May 10, 2010
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (2011) 4.42
Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (2012) 2.33
A de novo protein binding pair by computational design and directed evolution. Mol Cell (2011) 1.65
RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One (2011) 1.59
Accurate design of co-assembling multi-component protein nanomaterials. Nature (2014) 1.29
Computational design of a protein crystal. Proc Natl Acad Sci U S A (2012) 1.23
Molecular pathways: targeting p21-activated kinase 1 signaling in cancer--opportunities, challenges, and limitations. Clin Cancer Res (2012) 1.22
Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc (2011) 1.19
A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Sci (2012) 1.17
On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface (2012) 1.16
Computational design of a symmetric homodimer using β-strand assembly. Proc Natl Acad Sci U S A (2011) 1.12
Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Sci (2011) 1.10
Engineering a protein-protein interface using a computationally designed library. Proc Natl Acad Sci U S A (2010) 1.03
Computational design of a protein-based enzyme inhibitor. J Mol Biol (2013) 0.98
Anchored design of protein-protein interfaces. PLoS One (2011) 0.96
Therapeutic protein aggregation: mechanisms, design, and control. Trends Biotechnol (2014) 0.95
AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences. Proteins (2015) 0.86
Untangling the complexity of PAK1 dynamics: The future challenge. Cell Logist (2012) 0.85
Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding. Proteins (2013) 0.84
Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications. J Mol Biol (2011) 0.84
An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network. Protein Eng Des Sel (2014) 0.83
Strategies to control the binding mode of de novo designed protein interactions. Curr Opin Struct Biol (2013) 0.79
Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA. Protein Sci (2011) 0.79
A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins. Protein Eng Des Sel (2013) 0.78
3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers. Cell Logist (2012) 0.78
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
P21-activated kinase in inflammatory and cardiovascular disease. Cell Signal (2014) 0.78
A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. J Mol Biol (2014) 0.78
Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. Proteins (2014) 0.77
Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease. PLoS One (2014) 0.77
In silico analysis and experimental verification of OSR1 kinase - Peptide interaction. J Struct Biol (2014) 0.75
Scratching the Surface: Resurfacing Proteins to Endow New Properties and Function. Cell Chem Biol (2016) 0.75
A workflow for in silico design of hIL-10 and ebvIL-10 inhibitors using well-known miniprotein scaffolds. J Mol Model (2017) 0.75
NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR (1995) 93.94
Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene (1989) 60.30
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR (1995) 12.25
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
BioMagResBank. Nucleic Acids Res (2007) 10.21
Effective energy function for proteins in solution. Proteins (1999) 9.44
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol (2003) 8.35
Macromolecular modeling with rosetta. Annu Rev Biochem (2008) 8.32
Kemp elimination catalysts by computational enzyme design. Nature (2008) 8.19
Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A (2000) 7.99
Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci (1997) 7.92
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene (1995) 7.42
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins (1999) 4.86
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol (2003) 4.63
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Structure of PAK1 in an autoinhibited conformation reveals a multistage activation switch. Cell (2000) 4.21
High-resolution protein design with backbone freedom. Science (1998) 3.54
High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol (2004) 3.34
Automated design of specificity in molecular recognition. Nat Struct Biol (2003) 3.10
Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des (1998) 2.96
Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature (2009) 2.88
Computational design of protein-protein interactions. Curr Opin Chem Biol (2004) 2.39
De novo protein structure determination using sparse NMR data. J Biomol NMR (2000) 2.37
E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nat Struct Mol Biol (2005) 2.33
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
Electrostatic rate enhancement and transient complex of protein-protein association. Proteins (2008) 1.89
Biomolecular diffusional association. Curr Opin Struct Biol (2002) 1.78
Allosteric inhibition of aminoglycoside phosphotransferase by a designed ankyrin repeat protein. Structure (2005) 1.75
Computer-aided design of functional protein interactions. Nat Chem Biol (2009) 1.73
Computational design of affinity and specificity at protein-protein interfaces. Curr Opin Struct Biol (2009) 1.59
A de novo designed protein protein interface. Protein Sci (2007) 1.41
X-ray structure of the human hyperplastic discs protein: an ortholog of the C-terminal domain of poly(A)-binding protein. Proc Natl Acad Sci U S A (2001) 1.40
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
Adaptation of a fast Fourier transform-based docking algorithm for protein design. J Comput Chem (2005) 0.99
Maintaining solvent accessible surface area under rotamer substitution for protein design. J Comput Chem (2007) 0.88
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res (2007) 37.31
Predicting protein structures with a multiplayer online game. Nature (2010) 9.95
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol (2003) 8.35
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
A genetically encoded photoactivatable Rac controls the motility of living cells. Nature (2009) 7.25
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86
GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc (2003) 3.21
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol (2003) 3.08
Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proc Natl Acad Sci U S A (2008) 3.08
Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol (2002) 3.06
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
Eris: an automated estimator of protein stability. Nat Methods (2007) 2.78
Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins (2010) 2.56
Engineered allosteric activation of kinases in living cells. Nat Biotechnol (2010) 2.44
Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell (2009) 2.40
Emergence of protein fold families through rational design. PLoS Comput Biol (2006) 2.35
E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nat Struct Mol Biol (2005) 2.33
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
Recognition and processing of cisplatin- and oxaliplatin-DNA adducts. Crit Rev Oncol Hematol (2005) 2.16
NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci U S A (2005) 2.09
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
Designing photoswitchable peptides using the AsLOV2 domain. Chem Biol (2012) 1.99
An adaptive dynamic programming algorithm for the side chain placement problem. Pac Symp Biocomput (2005) 1.95
An improved protein decoy set for testing energy functions for protein structure prediction. Proteins (2003) 1.94
Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate. Mol Cell (2011) 1.92
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function. Nat Struct Mol Biol (2012) 1.76
High-resolution design of a protein loop. Proc Natl Acad Sci U S A (2007) 1.68
Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc (2006) 1.66
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol (2002) 1.66
Modeling backbone flexibility improves protein stability estimation. Structure (2007) 1.65
Automated minimization of steric clashes in protein structures. Proteins (2011) 1.64
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. J Biol Chem (2008) 1.62
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins (2005) 1.62
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
De novo enzyme design using Rosetta3. PLoS One (2011) 1.59
Computational design of affinity and specificity at protein-protein interfaces. Curr Opin Struct Biol (2009) 1.59
Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol (2013) 1.59
Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J (2002) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Modeling symmetric macromolecular structures in Rosetta3. PLoS One (2011) 1.52
Mechanism for the alpha-helix to beta-hairpin transition. Proteins (2003) 1.51
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One (2013) 1.49
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J Mol Biol (2006) 1.49
RosettaDesign server for protein design. Nucleic Acids Res (2006) 1.49
Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. J Mol Biol (2007) 1.48
Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci U S A (2009) 1.47
Design of protein conformational switches. Curr Opin Struct Biol (2006) 1.46
The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A (2004) 1.46
Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. J Biol Chem (2009) 1.46
Can contact potentials reliably predict stability of proteins? J Mol Biol (2004) 1.44
Computer-based design of novel protein structures. Annu Rev Biophys Biomol Struct (2006) 1.44
G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment. Proc Natl Acad Sci U S A (2004) 1.43
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
Oligo(N-aryl glycines): a new twist on structured peptoids. J Am Chem Soc (2008) 1.37
MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model (2008) 1.37
Rapid NMR data collection. Methods Enzymol (2005) 1.35
An integrated platform for automated analysis of protein NMR structures. Methods Enzymol (2005) 1.35
Design of a switchable eliminase. Proc Natl Acad Sci U S A (2011) 1.34
Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Proc Natl Acad Sci U S A (2013) 1.34
Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell (2003) 1.33
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. J Mol Biol (2010) 1.31
Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy. J Am Chem Soc (2011) 1.30
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J (2004) 1.29
A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell (2007) 1.28
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Elife (2013) 1.27
Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A (2006) 1.26
Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proc Natl Acad Sci U S A (2006) 1.25
Imprint of evolution on protein structures. Proc Natl Acad Sci U S A (2004) 1.24
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation. Proc Natl Acad Sci U S A (2008) 1.23
Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc (2010) 1.23
The path of DNA in the kinetochore. Curr Biol (2006) 1.22
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Structure-based design of supercharged, highly thermoresistant antibodies. Chem Biol (2012) 1.19
Sequence determinants of E2-E6AP binding affinity and specificity. J Mol Biol (2007) 1.19
Metal templated design of protein interfaces. Proc Natl Acad Sci U S A (2009) 1.19
Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc (2011) 1.19
G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination. J Am Chem Soc (2005) 1.18
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol (2005) 1.18
Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. J Mol Biol (2012) 1.18
RAP uses a histidine switch to regulate its interaction with LRP in the ER and Golgi. Mol Cell (2006) 1.18
Development of α-helical calpain probes by mimicking a natural protein-protein interaction. J Am Chem Soc (2012) 1.18
Protein folding: then and now. Arch Biochem Biophys (2007) 1.18