Published in Biopolymers on February 03, 2012
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CASP11 - An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. PLoS One (2016) 0.77
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Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput Biol Chem (2012) 0.75
Constraint methods that accelerate free-energy simulations of biomolecules. J Chem Phys (2015) 0.75
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Modeling structurally variable regions in homologous proteins with rosetta. Proteins (2004) 3.64
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Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
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Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci U S A (2003) 1.90
Contact order and ab initio protein structure prediction. Protein Sci (2002) 1.59
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Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol (2009) 1.11
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
New algorithms and an in silico benchmark for computational enzyme design. Protein Sci (2006) 3.40
Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy. J Mol Biol (2011) 3.16
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
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Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel. Biochemistry (2008) 2.22
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
Elucidating the ticking of an in vitro circadian clockwork. PLoS Biol (2007) 2.19
Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding. Structure (2008) 2.17
Crystal structure of human adenovirus at 3.5 A resolution. Science (2010) 2.17
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
Interaction of a G protein with an activated receptor opens the interdomain interface in the alpha subunit. Proc Natl Acad Sci U S A (2011) 2.10
Coagulation factor X activates innate immunity to human species C adenovirus. Science (2012) 2.09
Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments. J Virol (2006) 1.96
De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure (2008) 1.84
Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science (2014) 1.81
Structure and mechanism of protein stability sensors: chaperone activity of small heat shock proteins. Biochemistry (2009) 1.71
Model-free analysis of protein backbone motion from residual dipolar couplings. J Am Chem Soc (2002) 1.65
Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods. EMBO J (2006) 1.59
Discovery and characterization of novel subtype-selective allosteric agonists for the investigation of M(1) receptor function in the central nervous system. ACS Chem Neurosci (2010) 1.52
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RosettaEPR: an integrated tool for protein structure determination from sparse EPR data. J Struct Biol (2010) 1.50
Flexibility of the adenovirus fiber is required for efficient receptor interaction. J Virol (2003) 1.49
Development of a selective small-molecule inhibitor of Kir1.1, the renal outer medullary potassium channel. Mol Pharmacol (2010) 1.45
Postentry neutralization of adenovirus type 5 by an antihexon antibody. J Virol (2004) 1.40
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Cryoelectron microscopy imaging of recombinant and tissue derived vaults: localization of the MVP N termini and VPARP. J Mol Biol (2004) 1.39
CASP6 assessment of contact prediction. Proteins (2005) 1.39
Structural models for the KCNQ1 voltage-gated potassium channel. Biochemistry (2007) 1.38
A model for the solution structure of the rod arrestin tetramer. Structure (2008) 1.37
Engineering of vault nanocapsules with enzymatic and fluorescent properties. Proc Natl Acad Sci U S A (2005) 1.35
CryoEM structure at 9A resolution of an adenovirus vector targeted to hematopoietic cells. J Mol Biol (2005) 1.35
Insight into the mechanisms of adenovirus capsid disassembly from studies of defensin neutralization. PLoS Pathog (2010) 1.34
A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J Biomol NMR (2006) 1.34
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure (2009) 1.32
Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies. Proteins (2009) 1.32
Allosteric modulation of metabotropic glutamate receptors: structural insights and therapeutic potential. Neuropharmacology (2010) 1.30
Structural insights into a circadian oscillator. Science (2008) 1.30
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
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Cryo-electron microscopy structure of adenovirus type 2 temperature-sensitive mutant 1 reveals insight into the cell entry defect. J Virol (2009) 1.27
Conformation of receptor-bound visual arrestin. Proc Natl Acad Sci U S A (2012) 1.24
Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J (2008) 1.19
Identification of Metabotropic Glutamate Receptor Subtype 5 Potentiators Using Virtual High-Throughput Screening. ACS Chem Neurosci (2010) 1.16
EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure (2012) 1.15
Benchmarking ligand-based virtual High-Throughput Screening with the PubChem database. Molecules (2013) 1.14
Solvent accessible surface area approximations for rapid and accurate protein structure prediction. J Mol Model (2009) 1.14
Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solution. Angew Chem Int Ed Engl (2007) 1.13
Targeting vault nanoparticles to specific cell surface receptors. ACS Nano (2009) 1.13
Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol (2009) 1.11
The high-resolution solution structure of epothilone A bound to tubulin: an understanding of the structure-activity relationships for a powerful class of antitumor agents. Angew Chem Int Ed Engl (2003) 1.09
Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitin. Angew Chem Int Ed Engl (2005) 1.09
Cryo-electron microscopy structure of an adenovirus-integrin complex indicates conformational changes in both penton base and integrin. J Virol (2009) 1.08
HIV antigen incorporation within adenovirus hexon hypervariable 2 for a novel HIV vaccine approach. PLoS One (2010) 1.07
Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects. Retrovirology (2012) 1.06
Combined SAXS/EM based models of the S. elongatus post-translational circadian oscillator and its interactions with the output His-kinase SasA. PLoS One (2011) 1.05
Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: a perspective. J Mol Biol (2013) 1.05
Probing the metabotropic glutamate receptor 5 (mGlu₅) positive allosteric modulator (PAM) binding pocket: discovery of point mutations that engender a "molecular switch" in PAM pharmacology. Mol Pharmacol (2013) 1.05
The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping. Angew Chem Int Ed Engl (2005) 1.04
Rosetta Ligand docking with flexible XML protocols. Methods Mol Biol (2012) 1.04
Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J Struct Biol (2010) 1.02
BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. PLoS One (2012) 1.01
The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating. Channels (Austin) (2009) 1.01
The tubulin-bound conformation of discodermolide derived by NMR studies in solution supports a common pharmacophore model for epothilone and discodermolide. Angew Chem Int Ed Engl (2006) 1.01
CryoEM and molecular dynamics of the circadian KaiB-KaiC complex indicates that KaiB monomers interact with KaiC and block ATP binding clefts. J Mol Biol (2013) 1.00
Morphology of air nanobubbles trapped at hydrophobic nanopatterned surfaces. Nano Lett (2010) 1.00
BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements. PLoS One (2012) 1.00
Cryoelectron microscopy and EPR analysis of engineered symmetric and polydisperse Hsp16.5 assemblies reveals determinants of polydispersity and substrate binding. J Biol Chem (2006) 1.00
Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins (2013) 1.00
Nanoimprint-induced molecular orientation in semiconducting polymer nanostructures. ACS Nano (2011) 0.99
Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins (2004) 0.98
Human rotavirus VP6-specific antibodies mediate intracellular neutralization by binding to a quaternary structure in the transcriptional pore. PLoS One (2013) 0.98
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking. Proteins (2010) 0.97
Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. Prog Nucl Magn Reson Spectrosc (2011) 0.96
Bound to be different: neurotransmitter transporters meet their bacterial cousins. Mol Interv (2007) 0.96
A Script-Assisted Microscopy (SAM) package to improve data acquisition rates on FEI Tecnai electron microscopes equipped with Gatan CCD cameras. J Struct Biol (2008) 0.96
Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site. Immunome Res (2007) 0.96
A conserved asparagine residue in transmembrane segment 1 (TM1) of serotonin transporter dictates chloride-coupled neurotransmitter transport. J Biol Chem (2011) 0.96
A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics. Chembiochem (2002) 0.96
Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc (2013) 0.96
BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J Struct Biol (2011) 0.95
Structure of flexible filamentous plant viruses. J Virol (2008) 0.95
A unified hydrophobicity scale for multispan membrane proteins. Proteins (2009) 0.92
Characterization and modeling of the oligomeric state and ligand binding behavior of purified translocator protein 18 kDa from Rhodobacter sphaeroides. Biochemistry (2013) 0.92
Human antibodies that neutralize respiratory droplet transmissible H5N1 influenza viruses. J Clin Invest (2013) 0.92
Structure of human adenovirus. Curr Opin Virol (2012) 0.91