Published in PLoS One on May 21, 2013
Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins (2014) 1.05
EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib. Cancer Discov (2015) 0.96
On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures. Protein Sci (2016) 0.90
Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. PLoS One (2014) 0.88
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One (2015) 0.82
Native proteins trap high-energy transit conformations. Sci Adv (2015) 0.82
Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts. Proc Natl Acad Sci U S A (2016) 0.81
An efficient algorithm to perform local concerted movements of a chain molecule. PLoS One (2015) 0.81
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput Biol (2015) 0.80
Conformational stability of digestion-resistant peptides of peanut conglutins reveals the molecular basis of their allergenicity. Sci Rep (2016) 0.80
CASP11 refinement experiments with ROSETTA. Proteins (2015) 0.79
RCD+: Fast loop modeling server. Nucleic Acids Res (2016) 0.78
The origin of consistent protein structure refinement from structural averaging. Structure (2015) 0.77
The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone. PLoS One (2013) 0.77
Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation. Sci Signal (2017) 0.76
Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint. J Immunol (2016) 0.76
Algorithms for protein design. Curr Opin Struct Biol (2016) 0.76
Constraint methods that accelerate free-energy simulations of biomolecules. J Chem Phys (2015) 0.75
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics (2017) 0.75
"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. J Comput Chem (2017) 0.75
Modeling and docking of antibody structures with Rosetta. Nat Protoc (2017) 0.75
Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics (2017) 0.75
Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme. Mol Cell Biol (2016) 0.75
Antibody H3 Structure Prediction. Comput Struct Biotechnol J (2017) 0.75
Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res (2017) 0.75
Optimization by simulated annealing. Science (1983) 71.02
MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol (1997) 10.38
Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18
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
Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci (1997) 7.92
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol (1997) 4.79
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Rotamer libraries in the 21st century. Curr Opin Struct Biol (2002) 4.09
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods (2009) 3.25
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci U S A (1998) 2.92
Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci U S A (1999) 2.66
Principles for designing ideal protein structures. Nature (2012) 2.50
Progress and challenges in high-resolution refinement of protein structure models. Proteins (2005) 2.28
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (2011) 2.17
Toward better refinement of comparative models: predicting loops in inexact environments. Proteins (2008) 2.06
Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins (2010) 1.89
Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature (1998) 1.75
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput (2008) 1.72
High-resolution design of a protein loop. Proc Natl Acad Sci U S A (2007) 1.68
RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One (2011) 1.59
De novo enzyme design using Rosetta3. PLoS One (2011) 1.59
Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol (2013) 1.59
Alteration of enzyme specificity by computational loop remodeling and design. Proc Natl Acad Sci U S A (2009) 1.56
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol (2010) 1.44
Sampling bottlenecks in de novo protein structure prediction. J Mol Biol (2009) 1.40
Generalized fragment picking in Rosetta: design, protocols and applications. PLoS One (2011) 1.35
Backbone flexibility in computational protein design. Curr Opin Biotechnol (2009) 1.26
Protein loop modeling by using fragment assembly and analytical loop closure. Proteins (2010) 1.25
Role of the biomolecular energy gap in protein design, structure, and evolution. Cell (2012) 1.24
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A (2011) 1.23
Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins (2012) 1.21
Four small puzzles that Rosetta doesn't solve. PLoS One (2011) 1.19
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A (2012) 1.13
Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc (2012) 1.08
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J Comput Chem (2012) 1.08
Progress in super long loop prediction. Proteins (2011) 0.94
Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics (2005) 0.89
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol (2006) 4.52
Global landscape of HIV-human protein complexes. Nature (2011) 3.70
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods (2009) 3.25
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A (2004) 2.71
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol (2008) 2.27
Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell (2002) 2.25
SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane. J Cell Biol (2010) 2.10
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol (2006) 1.93
Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure (2003) 1.81
Computer-aided design of functional protein interactions. Nat Chem Biol (2009) 1.73
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins (2005) 1.62
Protein-protein docking predictions for the CAPRI experiment. Proteins (2003) 1.60
Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol (2013) 1.59
A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A (2006) 1.57
A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme. Cell (2011) 1.56
Design of multi-specificity in protein interfaces. PLoS Comput Biol (2007) 1.49
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One (2013) 1.49
Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Mol Cell (2003) 1.38
Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol (2010) 1.32
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol (2009) 1.27
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res (2004) 1.27
Backbone flexibility in computational protein design. Curr Opin Biotechnol (2009) 1.26
Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem (2005) 1.24
A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol (2008) 1.23
Cost-benefit tradeoffs in engineered lac operons. Science (2012) 1.21
Simple physical models connect theory and experiment in protein folding kinetics. J Mol Biol (2002) 1.20
Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure (2008) 1.20
RosettaBackrub--a web server for flexible backbone protein structure modeling and design. Nucleic Acids Res (2010) 1.16
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput (2015) 1.15
Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A (2012) 1.13
In support of the BMRB. Nat Struct Mol Biol (2012) 1.09
Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins (2009) 1.05
Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One (2011) 1.04
Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A (2006) 1.02
Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol (2013) 1.00
Computational protein design quantifies structural constraints on amino acid covariation. PLoS Comput Biol (2013) 0.99
Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. J Biol Chem (2007) 0.98
Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure (2007) 0.95
Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol (2010) 0.94
A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J Mol Biol (2007) 0.94
Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface. Protein Sci (2011) 0.92
Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Mol Syst Biol (2009) 0.92
Designing ensembles in conformational and sequence space to characterize and engineer proteins. Curr Opin Struct Biol (2010) 0.90
Potential functions for hydrogen bonds in protein structure prediction and design. Adv Protein Chem (2005) 0.90
Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs. J Biol Chem (2008) 0.89
Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol (2013) 0.89
Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1. Structure (2009) 0.88
Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol (2012) 0.87
Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry (2004) 0.86
Amino-acid site variability among natural and designed proteins. PeerJ (2013) 0.82
Design of a photoswitchable cadherin. J Am Chem Soc (2013) 0.80
Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure (2012) 0.78
The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput (2017) 0.76