Published in Pac Symp Biocomput on January 01, 2005
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res (2007) 37.31
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. PLoS Comput Biol (2012) 1.40
Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One (2011) 1.04
A generic program for multistate protein design. PLoS One (2011) 1.03
The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite. PLoS One (2013) 0.91
Rotamer optimization for protein design through MAP estimation and problem-size reduction. J Comput Chem (2009) 0.86
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J Comput Biol (2016) 0.80
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
Design of symmetric TIM barrel proteins from first principles. BMC Biochem (2015) 0.78
Fast search algorithms for computational protein design. J Comput Chem (2016) 0.76
A critical analysis of computational protein design with sparse residue interaction graphs. PLoS Comput Biol (2017) 0.75
MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory. PLoS Comput Biol (2017) 0.75
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res (2007) 37.31
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
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. J Math Biol (2007) 4.12
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol (2003) 3.08
Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell (2009) 2.40
E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nat Struct Mol Biol (2005) 2.33
Designing photoswitchable peptides using the AsLOV2 domain. Chem Biol (2012) 1.99
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
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
A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins (2005) 1.62
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
Computational design of a PAK1 binding protein. J Mol Biol (2010) 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
Design of protein conformational switches. Curr Opin Struct Biol (2006) 1.46
Computer-based design of novel protein structures. Annu Rev Biophys Biomol Struct (2006) 1.44
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
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
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
A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Sci (2012) 1.17
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput (2015) 1.15
Computational design of a symmetric homodimer using β-strand assembly. Proc Natl Acad Sci U S A (2011) 1.12
A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase. Structure (2007) 1.10
A biosensor generated via high-throughput screening quantifies cell edge Src dynamics. Nat Chem Biol (2011) 1.09
Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer. Biochemistry (2006) 1.06
Computational design of second-site suppressor mutations at protein-protein interfaces. Proteins (2010) 1.04
Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering. Biochemistry (2012) 1.04
A generic program for multistate protein design. PLoS One (2011) 1.03
Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins (2006) 1.03
Engineering a protein-protein interface using a computationally designed library. Proc Natl Acad Sci U S A (2010) 1.03
Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. PLoS One (2012) 1.02
Comparing graph representations of protein structure for mining family-specific residue-based packing motifs. J Comput Biol (2005) 1.01
Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design. Structure (2008) 1.01
Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. J Biol Chem (2010) 0.99
A preliminary survey of the peptoid folding landscape. J Am Chem Soc (2009) 0.98
Computational design of the sequence and structure of a protein-binding peptide. J Am Chem Soc (2011) 0.95
Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS One (2013) 0.94
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PLoS One (2013) 0.94
Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J Mol Biol (2006) 0.93
Computational protein design with explicit consideration of surface hydrophobic patches. Proteins (2011) 0.92
Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Sci (2002) 0.92
G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. J Biol Chem (2009) 0.91
Supertertiary structure of the MAGUK core from PSD-95. Structure (2013) 0.90
Kinetics of the transfer of ubiquitin from UbcH7 to E6AP. Biochemistry (2010) 0.90
Structure-based function inference using protein family-specific fingerprints. Protein Sci (2006) 0.88
Hold me tightly LOV. Nat Methods (2010) 0.88
Maintaining solvent accessible surface area under rotamer substitution for protein design. J Comput Chem (2007) 0.88
Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core. Structure (2012) 0.87
Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants. J Biol Chem (2010) 0.86
Distance-based identification of structure motifs in proteins using constrained frequent subgraph mining. Comput Syst Bioinformatics Conf (2006) 0.86
The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed. Biol Direct (2014) 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
Computational de novo design of a four-helix bundle protein--DND_4HB. Protein Sci (2014) 0.82
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. J Comput Aided Mol Des (2009) 0.82
Using quantum mechanics to improve estimates of amino acid side chain rotamer energies. Proteins (2008) 0.82
Fab-based bispecific antibody formats with robust biophysical properties and biological activity. MAbs (2015) 0.81
Defining and computing optimum RMSD for gapped and weighted multiple-structure alignment. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.80
Strategies to control the binding mode of de novo designed protein interactions. Curr Opin Struct Biol (2013) 0.79
Biochemistry. From computational design to a protein that binds. Science (2011) 0.79
Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. Biochemistry (2016) 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
Cages from coils. Nat Biotechnol (2013) 0.77
Artifacts caused by simplicial subdivision. IEEE Trans Vis Comput Graph (2006) 0.77
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. J Comput Aided Mol Des (2009) 0.77
Using anchoring motifs for the computational design of protein-protein interactions. Biochem Soc Trans (2013) 0.76
Multiple structure alignment by optimal RMSD implies that the average structure is a consensus. Comput Syst Bioinformatics Conf (2006) 0.76
The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput (2017) 0.76
Redesigning the NEDD8 pathway with a bacterial genetic screen for ubiquitin-like molecule transfer. J Mol Biol (2012) 0.75
Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. IEEE Trans Inf Technol Biomed (2010) 0.75
Engineering and design: editorial overview. Curr Opin Struct Biol (2009) 0.75
Functional Class I and II amino acid-activating enzymes can be coded by opposite strands of the same gene. J Biol Chem (2016) 0.75