Published in Structure on September 12, 2013
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell (2014) 2.71
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife (2014) 2.23
Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Cell (2015) 1.64
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat Methods (2015) 1.52
Protein structure determination using metagenome sequence data. Science (2017) 1.47
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat Chem Biol (2015) 1.45
Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2. Nat Struct Mol Biol (2017) 1.40
Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. Science (2016) 1.39
Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Science (2016) 1.36
Structure of the type VI secretion system contractile sheath. Cell (2015) 1.28
Large-scale determination of previously unsolved protein structures using evolutionary information. Elife (2015) 1.14
Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature (2016) 1.12
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane. Cell (2017) 1.09
De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nat Methods (2015) 1.05
The Cer-cqu gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes. J Exp Bot (2016) 1.00
Virology. A virus that infects a hyperthermophile encapsidates A-form DNA. Science (2015) 0.99
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Proteins (2013) 0.97
The molecular basis for flexibility in the flexible filamentous plant viruses. Nat Struct Mol Biol (2015) 0.97
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
Control of repeat-protein curvature by computational protein design. Nat Struct Mol Biol (2015) 0.95
Structure of the voltage-gated calcium channel Cav1.1 at 3.6 Å resolution. Nature (2016) 0.91
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins (2016) 0.90
Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A (2015) 0.89
Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nat Struct Mol Biol (2016) 0.87
Homology modeling of larger proteins guided by chemical shifts. Nat Methods (2015) 0.86
A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein. Sci Rep (2016) 0.86
Functional analysis of drug resistance-associated mutations in the Trypanosoma brucei adenosine transporter 1 (TbAT1) and the proposal of a structural model for the protein. Mol Microbiol (2015) 0.84
Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Cell (2015) 0.83
Visualizing microtubule structural transitions and interactions with associated proteins. Curr Opin Struct Biol (2016) 0.83
Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. Proteins (2016) 0.83
The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core. Structure (2015) 0.82
Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells. J Biol Chem (2015) 0.82
Diverse role of Survival Motor Neuron Protein. Biochim Biophys Acta (2017) 0.81
Biophysical and structural characterization of the thioredoxin-binding domain of protein kinase ASK1 and its interaction with reduced thioredoxin. J Biol Chem (2014) 0.81
Structural and Immunological Characterization of Recombinant 6-Cysteine Domains of the Plasmodium falciparum Sexual Stage Protein Pfs230. J Biol Chem (2016) 0.81
Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res (2014) 0.80
Differential ubiquitin binding by the acidic loops of Ube2g1 and Ube2r1 enzymes distinguishes their Lys-48-ubiquitylation activities. J Biol Chem (2014) 0.79
CASP11 refinement experiments with ROSETTA. Proteins (2015) 0.79
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. J Chem Theory Comput (2016) 0.79
Rearrangement of the Extracellular Domain/Extracellular Loop 1 Interface Is Critical for Thyrotropin Receptor Activation. J Biol Chem (2016) 0.78
A Framework to Simplify Combined Sampling Strategies in Rosetta. PLoS One (2015) 0.78
Targeted Proteomics and Absolute Protein Quantification for the Construction of a Stoichiometric Host-Pathogen Surface Density Model. Mol Cell Proteomics (2017) 0.78
Rational design and validation of a vanilloid-sensitive TRPV2 ion channel. Proc Natl Acad Sci U S A (2016) 0.78
Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins (2016) 0.77
Structural insights into SAM domain-mediated tankyrase oligomerization. Protein Sci (2016) 0.77
The origin of consistent protein structure refinement from structural averaging. Structure (2015) 0.77
Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. Nat Struct Mol Biol (2015) 0.77
Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria. Appl Environ Microbiol (2016) 0.77
The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration. Nature (2016) 0.77
An electron microscopy journey in the study of microtubule structure and dynamics. Protein Sci (2015) 0.77
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts. Biochemistry (2016) 0.76
Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun (2015) 0.76
Structural characterization of the C-terminal coiled-coil domains of wild-type and kidney disease-associated mutants of apolipoprotein L1. FEBS J (2016) 0.76
Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy. Protein Sci (2016) 0.76
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. Comput Struct Biotechnol J (2015) 0.76
RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nat Methods (2017) 0.75
A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. F1000Res (2017) 0.75
Clustering and percolation in protein loop structures. BMC Struct Biol (2015) 0.75
Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4. Autophagy (2016) 0.75
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. PLoS Comput Biol (2016) 0.75
Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Nature (2016) 0.75
Amyotrophic Lateral Sclerosis Type 20 - In Silico Analysis and Molecular Dynamics Simulation of hnRNPA1. PLoS One (2016) 0.75
CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proc Natl Acad Sci U S A (2017) 0.75
GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. BMC Res Notes (2016) 0.75
Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res (2016) 0.75
Prostaglandin E2 glyceryl ester is an endogenous agonist of the nucleotide receptor P2Y6. Sci Rep (2017) 0.75
Rosetta and the Design of Ligand Binding Sites. Methods Mol Biol (2016) 0.75
Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. Open Biol (2017) 0.75
A structural model of flagellar filament switching across multiple bacterial species. Nat Commun (2017) 0.75
MEFA (multiepitope fusion antigen)-Novel Technology for Structural Vaccinology, Proof from Computational and Empirical Immunogenicity Characterization of an Enterotoxigenic Escherichia coli (ETEC) Adhesin MEFA. J Vaccines Vaccin (2017) 0.75
Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Elife (2017) 0.75
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature (2017) 0.75
Conformational Dynamics and Allostery in E2:E3 Interactions Drive Ubiquitination: gp78 and Ube2g2. Structure (2017) 0.75
The subtle allostery of microtubule dynamics. Nat Struct Mol Biol (2014) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res (2007) 37.31
The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res (2003) 9.44
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Macromolecular modeling with rosetta. Annu Rev Biochem (2008) 8.32
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06
Processing and analysis of CASP3 protein structure predictions. Proteins (1999) 4.95
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (2011) 4.42
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
Analysis and assessment of comparative modeling predictions in CASP4. Proteins (2001) 3.42
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A (2002) 3.23
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2010) 2.96
The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins (2009) 2.43
Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (2012) 2.33
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins (2004) 2.16
Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol (2010) 1.90
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins (2011) 1.58
Boosting Protein Threading Accuracy. Res Comput Mol Biol (2009) 1.17
DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci (2007) 1.14
Incorporation of evolutionary information into Rosetta comparative modeling. Proteins (2011) 1.05
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
Predicting protein structures with a multiplayer online game. Nature (2010) 9.95
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
Kemp elimination catalysts by computational enzyme design. Nature (2008) 8.19
Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol (2002) 7.79
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
De novo computational design of retro-aldol enzymes. Science (2008) 7.62
Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res (2004) 7.39
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A (2002) 6.18
Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol (2011) 5.02
Towards robust regional estimates of CO2 sources and sinks using atmospheric transport models. Nature (2002) 4.71
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol (2003) 4.63
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Stop Hypertension with the Acupuncture Research Program (SHARP): results of a randomized, controlled clinical trial. Hypertension (2006) 4.54
Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol (2006) 4.52
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (2011) 4.42
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science (2010) 4.32
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins (2009) 4.27
Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 4.06
Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature (2010) 4.04
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
Algorithm discovery by protein folding game players. Proc Natl Acad Sci U S A (2011) 3.74
Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol (2004) 3.66
Modeling structurally variable regions in homologous proteins with rosetta. Proteins (2004) 3.64
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
The role of inflammation in the pathogenesis of age-related macular degeneration. Surv Ophthalmol (2006) 3.60
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins (2006) 3.60
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature (2011) 3.56
Rational HIV immunogen design to target specific germline B cell receptors. Science (2013) 3.55
Noncanonical TGFβ signaling contributes to aortic aneurysm progression in Marfan syndrome mice. Science (2011) 3.49
High-resolution mapping of protein sequence-function relationships. Nat Methods (2010) 3.47
Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature (2006) 3.45
Computational alanine scanning of protein-protein interfaces. Sci STKE (2004) 3.41
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
New algorithms and an in silico benchmark for computational enzyme design. Protein Sci (2006) 3.40
Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature (2012) 3.38
Simplification of antiretroviral therapy with tenofovir-emtricitabine or abacavir-Lamivudine: a randomized, 96-week trial. Clin Infect Dis (2009) 3.32
Inflammation in neurodegenerative diseases. Immunology (2010) 3.22
An engineered microbial platform for direct biofuel production from brown macroalgae. Science (2012) 3.20
Clinical outcomes after lumbar discectomy for sciatica: the effects of fragment type and anular competence. J Bone Joint Surg Am (2003) 3.14
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol (2003) 3.08
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
Progress in modeling of protein structures and interactions. Science (2005) 3.05
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci U S A (2009) 3.01
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007) 3.01
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A (2006) 2.88
De novo prediction of three-dimensional structures for major protein families. J Mol Biol (2002) 2.88
RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol (2008) 2.86
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci U S A (2006) 2.81
Multipass membrane protein structure prediction using Rosetta. Proteins (2006) 2.79
Computational thermostabilization of an enzyme. Science (2005) 2.79
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
Improved molecular replacement by density- and energy-guided protein structure optimization. Nature (2011) 2.74
Improved side-chain modeling for protein-protein docking. Protein Sci (2005) 2.72
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
Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A (2010) 2.68
Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins (2010) 2.56
CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods (2009) 2.50
A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell (2007) 2.50
Principles for designing ideal protein structures. Nature (2012) 2.50
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature (2011) 2.49
Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A (2006) 2.47
Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature (2011) 2.46
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Heterologous expression of proteins from Plasmodium falciparum: results from 1000 genes. Mol Biochem Parasitol (2006) 2.45
De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR (2008) 2.43
No effect of rosiglitazone for treatment of HIV-1 lipoatrophy: randomised, double-blind, placebo-controlled trial. Lancet (2004) 2.43
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A (2013) 2.43
Computational design of protein-protein interactions. Curr Opin Chem Biol (2004) 2.39
Contact order revisited: influence of protein size on the folding rate. Protein Sci (2003) 2.37
Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci U S A (2007) 2.35
Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (2012) 2.33
Progress and challenges in high-resolution refinement of protein structure models. Proteins (2005) 2.28
Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell (2002) 2.25
Droplet interface bilayers. Mol Biosyst (2008) 2.23
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature (2011) 2.20
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol (2012) 2.19
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (2011) 2.17
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol (2012) 2.14
De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc (2002) 2.12
Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol (2011) 2.12
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins (2006) 2.07