Published in J Comput Aided Mol Des on November 01, 2003
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics (2008) 1.88
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. Nucleic Acids Res (2009) 1.38
Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins (2005) 1.24
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics (2011) 1.15
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct Biol (2008) 1.07
Theoretical model of prion propagation: a misfolded protein induces misfolding. Proc Natl Acad Sci U S A (2005) 1.02
NPDock: a web server for protein-nucleic acid docking. Nucleic Acids Res (2015) 0.95
The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics (2013) 0.95
Modeling of loops in proteins: a multi-method approach. BMC Struct Biol (2010) 0.91
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. PLoS Comput Biol (2012) 0.89
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res (2013) 0.89
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC Struct Biol (2008) 0.88
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res (2015) 0.86
Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation. Nat Commun (2014) 0.86
Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. Structure (2015) 0.84
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid. J Steroid Biochem Mol Biol (2010) 0.81
The architecture of the Schizosaccharomyces pombe CCR4-NOT complex. Nat Commun (2016) 0.81
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement. BMC Bioinformatics (2012) 0.81
Structure prediction of the second extracellular loop in G-protein-coupled receptors. Biophys J (2014) 0.80
Identification of STAT1 and STAT3 specific inhibitors using comparative virtual screening and docking validation. PLoS One (2015) 0.79
QA-RecombineIt: a server for quality assessment and recombination of protein models. Nucleic Acids Res (2013) 0.79
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophys J (2008) 0.78
Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2. FEBS Open Bio (2014) 0.78
Rational engineering of sequence specificity in R.MwoI restriction endonuclease. Nucleic Acids Res (2012) 0.77
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinformatics (2015) 0.75
Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII. Nucleic Acids Res (2012) 0.75
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics (2011) 0.75
Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p. Cell Cycle (2011) 0.75
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Protein structure prediction and structural genomics. Science (2001) 11.76
Modeling of loops in protein structures. Protein Sci (2000) 9.68
Structural genomics and its importance for gene function analysis. Nat Biotechnol (2000) 3.70
100,000 protein structures for the biologist. Nat Struct Biol (1998) 3.19
Prospects for ab initio protein structural genomics. J Mol Biol (2001) 2.43
Protein structure computing in the genomic era. Res Microbiol (2000) 2.38
Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci (2000) 2.10
MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res (2002) 2.01
Structural genomics: a pipeline for providing structures for the biologist. Protein Sci (2002) 1.91
Protein NMR spectroscopy in structural genomics. Nat Struct Biol (2000) 1.80
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci U S A (2001) 1.80
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. Biophys J (1999) 1.68
Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins (2000) 1.63
New Monte Carlo algorithms for protein folding. Curr Opin Struct Biol (1999) 1.63
Contact order and ab initio protein structure prediction. Protein Sci (2002) 1.59
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins (1998) 1.53
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
Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins (2001) 1.12
Protein structure prediction in 2002. Curr Opin Struct Biol (2002) 1.11
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins (2001) 1.11
Knowledge-based model building of proteins: concepts and examples. Protein Sci (1993) 0.96
Local structure prediction with local structure-based sequence profiles. Bioinformatics (2003) 0.86
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
How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol (2003) 6.16
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
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
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
Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem (2008) 2.58
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
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem (2007) 1.71
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
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J Comput Chem (2007) 1.47
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
BioShell--a package of tools for structural biology computations. Bioinformatics (2006) 1.25
Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys J (2007) 1.25
The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One (2008) 1.25
Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins (2005) 1.24
Characterization of protein-folding pathways by reduced-space modeling. Proc Natl Acad Sci U S A (2007) 1.24
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
TOUCHSTONE: a unified approach to protein structure prediction. Proteins (2003) 1.20
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
Ideal amino acid exchange forms for approximating substitution matrices. Proteins (2007) 1.16
Utility library for structural bioinformatics. Bioinformatics (2008) 1.16
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct Biol (2007) 1.15
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
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Struct Biol (2007) 1.10
TASSER-based refinement of NMR structures. Proteins (2006) 1.09
Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol (2004) 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
ClusCo: clustering and comparison of protein models. BMC Bioinformatics (2013) 1.05
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
Theoretical model of prion propagation: a misfolded protein induces misfolding. Proc Natl Acad Sci U S A (2005) 1.02
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (2010) 1.01
DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responses. Cancer Res (2005) 1.00
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
CABS-flex: Server for fast simulation of protein structure fluctuations. Nucleic Acids Res (2013) 0.98
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
Exploring protein energy landscapes with hierarchical clustering. Int J Quantum Chem (2005) 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
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism. J Am Chem Soc (2011) 0.95
Performance of the Pro-sp3-TASSER server in CASP8. Proteins (2009) 0.95
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins (2011) 0.95
Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering. J Mol Biol (2009) 0.94
High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC Genomics (2006) 0.94