Published in J Comput Chem on July 15, 2008
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Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles. Proc Natl Acad Sci U S A (2010) 1.62
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SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci (2010) 1.01
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Three dimensional structure of the anthrax toxin translocon-lethal factor complex by cryo-electron microscopy. Protein Sci (2013) 0.90
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Interactions between a voltage sensor and a toxin via multiscale simulations. Biophys J (2010) 0.86
Incorporation of local structural preference potential improves fold recognition. PLoS One (2011) 0.85
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eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One (2012) 0.85
Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol (2014) 0.84
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High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape. Biophys J (2016) 0.80
Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state. Biophys Physicobiol (2016) 0.80
Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat. Front Plant Sci (2017) 0.80
On the role of physics and evolution in dictating protein structure and function. Isr J Chem (2014) 0.79
Improving consensus structure by eliminating averaging artifacts. BMC Struct Biol (2009) 0.79
Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex. PLoS One (2014) 0.79
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. J Biomol NMR (2012) 0.79
A multilayer evaluation approach for protein structure prediction and model quality assessment. Proteins (2011) 0.79
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol (2010) 0.78
Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein. Proc Natl Acad Sci U S A (2016) 0.78
A three dimensional visualisation approach to protein heavy-atom structure reconstruction. BMC Struct Biol (2014) 0.77
A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling. Sci Rep (2016) 0.77
Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput (2015) 0.77
Molecular dynamics trajectory compression with a coarse-grained model. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.76
Modeling disordered protein interactions from biophysical principles. PLoS Comput Biol (2017) 0.76
Adaptive firefly algorithm: parameter analysis and its application. PLoS One (2014) 0.75
Rapid chain tracing of polypeptide backbones in electron-density maps. Acta Crystallogr D Biol Crystallogr (2010) 0.75
Efficient conformational space exploration in ab initio protein folding simulation. R Soc Open Sci (2015) 0.75
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics (2016) 0.75
Selective refinement and selection of near-native models in protein structure prediction. Proteins (2015) 0.75
A scoring function based on solvation thermodynamics for protein structure prediction. Biophysics (Nagoya-shi) (2012) 0.75
Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins (2015) 0.75
Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem (2015) 0.75
Functional and structural insight into properdin control of complement alternative pathway amplification. EMBO J (2017) 0.75
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.). BMC Bioinformatics (2016) 0.75
TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. Proteins (2010) 0.75
Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment. Comput Biol Chem (2012) 0.75
An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophys J (2017) 0.75
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Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins (2000) 1.88
Analysis of TASSER-based CASP7 protein structure prediction results. Proteins (2007) 1.85
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Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem (2003) 1.27
Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Eng (2000) 1.09
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
Scoring function for automated assessment of protein structure template quality. Proteins (2004) 10.99
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Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem (2004) 4.87
TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J (2003) 4.62
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins (2002) 3.09
On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci U S A (2006) 2.85
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins (2005) 2.57
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins (2002) 2.42
Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol (2006) 2.40
The PDB is a covering set of small protein structures. J Mol Biol (2003) 2.26
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J (2004) 2.13
Analysis of TASSER-based CASP7 protein structure prediction results. Proteins (2007) 1.85
Development of unified statistical potentials describing protein-protein interactions. Biophys J (2003) 1.83
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EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res (2004) 1.70
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res (2008) 1.68
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics (2008) 1.50
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins (2004) 1.41
Efficient prediction of nucleic acid binding function from low-resolution protein structures. J Mol Biol (2006) 1.40
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinformatics (2009) 1.40
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J (2011) 1.39
FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol (2009) 1.38
All-atom ab initio folding of a diverse set of proteins. Structure (2007) 1.36
Identification of metabolites with anticancer properties by computational metabolomics. Mol Cancer (2008) 1.35
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem (2008) 1.34
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci U S A (2010) 1.34
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A (2002) 1.33
Ab initio protein structure prediction using chunk-TASSER. Biophys J (2007) 1.32
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res (2003) 1.32
Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28
Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des (2003) 1.26
The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One (2008) 1.25
Prediction of physical protein-protein interactions. Phys Biol (2005) 1.23
Assessment of programs for ligand binding affinity prediction. J Comput Chem (2008) 1.23
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics (2012) 1.23
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol (2009) 1.19
Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A (2008) 1.18
APoc: large-scale identification of similar protein pockets. Bioinformatics (2013) 1.18
iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (2010) 1.17
Development of a physics-based force field for the scoring and refinement of protein models. Biophys J (2008) 1.17
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins (2008) 1.16
Protein structure prediction by pro-Sp3-TASSER. Biophys J (2009) 1.12
Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins (2010) 1.11
What is the relationship between the global structures of apo and holo proteins? Proteins (2008) 1.10
TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins (2003) 1.10
Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol (2004) 1.09
TASSER-based refinement of NMR structures. Proteins (2006) 1.09
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model (2012) 1.09
Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Environ Microbiol (2007) 1.08
M-TASSER: an algorithm for protein quaternary structure prediction. Biophys J (2007) 1.08
A comprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol (2013) 1.04
Marker metabolites can be therapeutic targets as well. Nature (2008) 1.04
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J (2008) 1.03
TASSER-Lite: an automated tool for protein comparative modeling. Biophys J (2006) 1.03
Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations. J Chem Phys (2012) 1.02
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proc Natl Acad Sci U S A (2012) 1.02
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (2010) 1.01
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins (2010) 1.00
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem (2010) 0.99
Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers (2003) 0.99
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput Biol (2009) 0.98
Template-based protein structure modeling using TASSER(VMT.). Proteins (2011) 0.98
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. Mol Pharm (2012) 0.98
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. Biophys J (2003) 0.97
New benchmark metrics for protein-protein docking methods. Proteins (2011) 0.97
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins (2010) 0.97
Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase. Biochemistry (2007) 0.95
Performance of the Pro-sp3-TASSER server in CASP8. Proteins (2009) 0.95
High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC Genomics (2006) 0.94
Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions. Proteins (2007) 0.91
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. Phys Chem Chem Phys (2011) 0.91
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model (2010) 0.91
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol (2013) 0.89
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol (2013) 0.87
Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol Pharm (2010) 0.86
A scoring function for docking ligands to low-resolution protein structures. J Comput Chem (2005) 0.86
Benchmarking of TASSER in the ab initio limit. Proteins (2007) 0.86
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model. Biophys J (2003) 0.83
Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers (2003) 0.82
On the importance of hydrodynamic interactions in lipid membrane formation. Biophys J (2013) 0.82
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers (2003) 0.82
Docking of small ligands to low-resolution and theoretically predicted receptor structures. J Comput Chem (2002) 0.82
Benchmarking of dimeric threading and structure refinement. Proteins (2006) 0.81
TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets. Biophys J (2010) 0.81
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. Biophys J (2002) 0.78
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TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. Proteins (2010) 0.75
Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia. Mol Biosyst (2015) 0.75
How DNA medicines could transform treatment of glioblastoma multiforme. Am J Manag Care (2020) 0.75
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