Published in Sci Rep on January 01, 2013
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins (2015) 0.87
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling. PLoS Comput Biol (2015) 0.86
MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models. J Mol Model (2015) 0.80
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallogr D Struct Biol (2016) 0.80
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J Proteome Res (2015) 0.80
STRUM: structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics (2016) 0.79
General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model (2015) 0.78
Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol (2016) 0.75
A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive. PLoS One (2016) 0.75
Cysteine-Rich Atrial Secretory Protein from the Snail Achatina achatina: Purification and Structural Characterization. PLoS One (2015) 0.75
PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types. PLoS One (2016) 0.75
Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome. Front Mol Biosci (2017) 0.75
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics (2016) 0.75
Homology modeling in a dynamical world. Protein Sci (2017) 0.75
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol (2017) 0.75
Molecular and structural characteristics of multidrug resistance-associated protein 7 in Chinese liver fluke Clonorchis sinensis. Parasitol Res (2017) 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
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol (1970) 155.96
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
Rapid and sensitive protein similarity searches. Science (1985) 76.83
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
Profile hidden Markov models. Bioinformatics (1998) 56.04
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57
Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26
Position-based sequence weights. J Mol Biol (1994) 24.41
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
A method to identify protein sequences that fold into a known three-dimensional structure. Science (1991) 14.08
Protein structure prediction and structural genomics. Science (2001) 11.76
Scoring function for automated assessment of protein structure template quality. Proteins (2004) 10.99
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09
Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins (2000) 8.17
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
A comparison of scoring functions for protein sequence profile alignment. Bioinformatics (2004) 6.44
Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci (2000) 6.23
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods (2011) 6.06
Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A (1998) 4.17
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics (2003) 4.01
A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res (2002) 3.76
Progress and challenges in protein structure prediction. Curr Opin Struct Biol (2008) 3.48
Automated server predictions in CASP7. Proteins (2007) 3.40
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38
How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22
SABmark--a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics (2004) 3.11
Profile Comparer: a program for scoring and aligning profile hidden Markov models. Bioinformatics (2008) 2.94
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins (2003) 2.67
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34
Protein threading using PROSPECT: design and evaluation. Proteins (2000) 2.26
Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins (2004) 2.16
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (2011) 2.13
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res (2005) 1.95
Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol (2000) 1.80
CASP9 target classification. Proteins (2011) 1.75
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol (2007) 1.53
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci (2005) 1.38
A study on protein sequence alignment quality. Proteins (2002) 1.11
Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B (2012) 1.07
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. PLoS One (2008) 1.02
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep (2013) 0.88
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
IL-21 regulates germinal center B cell differentiation and proliferation through a B cell-intrinsic mechanism. J Exp Med (2010) 4.04
Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet (2010) 4.01
Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00
Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75
Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73
RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38
How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22
Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94
Three-field or two-field resection for thoracic esophageal cancer: a meta-analysis. Ann Thorac Surg (2013) 2.92
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75
Long noncoding RNAs with snoRNA ends. Mol Cell (2012) 2.71
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43
Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature (2003) 2.42
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41
Functional mesenchymal stem cells derived from human induced pluripotent stem cells attenuate limb ischemia in mice. Circulation (2010) 2.39
Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc Natl Acad Sci U S A (2006) 2.37
MicroRNA-101 inhibited postinfarct cardiac fibrosis and improved left ventricular compliance via the FBJ osteosarcoma oncogene/transforming growth factor-β1 pathway. Circulation (2012) 2.36
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34
Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33
Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24
Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17
HAb18G/CD147 promotes activation of hepatic stellate cells and is a target for antibody therapy of liver fibrosis. J Hepatol (2012) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Nat Genet (2011) 2.13
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
Pattern of lymphatic spread in thoracic esophageal squamous cell carcinoma: A single-institution experience. J Thorac Cardiovasc Surg (2012) 2.08
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol (2008) 1.96
Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics (2002) 1.81
Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80
Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics (2012) 1.80
Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death. Am J Physiol Lung Cell Mol Physiol (2007) 1.75
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques (2004) 1.74
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res (2013) 1.72
Photoaffinity isolation and identification of proteins in cancer cell extracts that bind to platinum-modified DNA. Chembiochem (2009) 1.71
Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res (2004) 1.71
The role of concurrent chemoradiotherapy in the treatment of locoregionally advanced nasopharyngeal carcinoma among endemic population: a meta-analysis of the phase III randomized trials. BMC Cancer (2010) 1.68
Gram-scale synthesis of submicrometer-long polythiophene wires in mesoporous silica matrices. Angew Chem Int Ed Engl (2003) 1.64
Efficacy of entecavir in chronic hepatitis B patients with mildly elevated alanine aminotransferase and biopsy-proven histological damage. Hepatology (2010) 1.61
Outcomes of the POG 9340/9341/9342 trials for children with high-risk neuroblastoma: a report from the Children's Oncology Group. Pediatr Blood Cancer (2008) 1.60
Long-term treatment with entecavir induces reversal of advanced fibrosis or cirrhosis in patients with chronic hepatitis B. Clin Gastroenterol Hepatol (2010) 1.60
Control of autophagy maturation by acid sphingomyelinase in mouse coronary arterial smooth muscle cells: protective role in atherosclerosis. J Mol Med (Berl) (2014) 1.59
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
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics (2010) 1.55
FGF21 and the late adaptive response to starvation in humans. J Clin Invest (2015) 1.55
Palladium-catalyzed enantioselective addition of two distinct nucleophiles across alkenes capable of quinone methide formation. J Am Chem Soc (2009) 1.54
Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54
Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics (2007) 1.53
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell (2012) 1.52
TRAIL death receptor 4 signaling via lysosome fusion and membrane raft clustering in coronary arterial endothelial cells: evidence from ASM knockout mice. J Mol Med (Berl) (2012) 1.52
HAb18G/CD147 functions in invasion and metastasis of hepatocellular carcinoma. Mol Cancer Res (2007) 1.48
CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol (2003) 1.47
No supernovae associated with two long-duration gamma-ray bursts. Nature (2006) 1.47
catena-Poly[[bis(thiocyanato-kappa N)cadmium(II)]-di-mu-thiourea-kappa(4)S:S]. Acta Crystallogr C (2002) 1.45
HAb18G (CD147), a cancer-associated biomarker and its role in cancer detection. Histopathology (2009) 1.45
SNP discovery by high-throughput sequencing in soybean. BMC Genomics (2010) 1.45
Potential role of human visceral pleura in pleural fluid turnover. Chin Med J (Engl) (2006) 1.44
Preoperative rosuvastatin protects patients with coronary artery disease undergoing noncardiac surgery. Cardiology (2015) 1.43
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure (2012) 1.42
Single feature polymorphism discovery in rice. PLoS One (2007) 1.42
MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42
Infant speech perception activates Broca's area: a developmental magnetoencephalography study. Neuroreport (2006) 1.40
SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics (2010) 1.39
Toxicity and cellular responses of intestinal cells exposed to titanium dioxide. Cell Biol Toxicol (2009) 1.38
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics (2008) 1.35
Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One (2009) 1.34
Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (2011) 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
BAFF overexpression and accelerated glomerular disease in mice with an incomplete genetic predisposition to systemic lupus erythematosus. Arthritis Rheum (2005) 1.33
P3DB: a plant protein phosphorylation database. Nucleic Acids Res (2008) 1.31
National survey of the medical treatment status for non-small cell lung cancer (NSCLC) in China. Lung Cancer (2012) 1.30
Legume transcription factor genes: what makes legumes so special? Plant Physiol (2009) 1.30
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol (2004) 1.30
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics (2012) 1.29
Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J Bacteriol (2007) 1.29
Critical role of lipid raft redox signaling platforms in endostatin-induced coronary endothelial dysfunction. Arterioscler Thromb Vasc Biol (2007) 1.29
Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28
Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol Plant Microbe Interact (2005) 1.27