Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement.

PubWeight™: 1.42‹?› | Rank: Top 5%

🔗 View Article (PMC 3372652)

Published in Structure on May 03, 2012

Authors

Ambrish Roy1, Yang Zhang

Author Affiliations

1: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

Articles citing this

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75

BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43

I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res (2015) 1.59

FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model (2012) 1.09

Functional site plasticity in domain superfamilies. Biochim Biophys Acta (2013) 1.00

The hepatitis E virus polyproline region is involved in viral adaptation. PLoS One (2012) 0.98

Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses. Sci Rep (2014) 0.96

Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr Opin Struct Biol (2013) 0.93

Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics (2013) 0.90

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol (2013) 0.89

An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. PLoS Comput Biol (2013) 0.85

Protein Structure and Function Prediction Using I-TASSER. Curr Protoc Bioinformatics (2015) 0.82

Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J Proteome Res (2015) 0.80

Structure-based Methods for Computational Protein Functional Site Prediction. Comput Struct Biotechnol J (2013) 0.80

Ligand binding site detection by local structure alignment and its performance complementarity. J Chem Inf Model (2013) 0.77

Structure prediction of partial-length protein sequences. Int J Mol Sci (2013) 0.77

Crystal structure of an arginase-like protein from Trypanosoma brucei that evolved without a binuclear manganese cluster. Biochemistry (2014) 0.76

Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J Cheminform (2015) 0.76

Protein depth calculation and the use for improving accuracy of protein fold recognition. J Comput Biol (2013) 0.76

Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. Res Comput Mol Biol (2013) 0.75

Predicting flavin and nicotinamide adenine dinucleotide-binding sites in proteins using the fragment transformation method. Biomed Res Int (2015) 0.75

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics (2016) 0.75

Protein ligand-specific binding residue predictions by an ensemble classifier. BMC Bioinformatics (2016) 0.75

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. Sci Rep (2017) 0.75

Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase. ScientificWorldJournal (2014) 0.75

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms. PLoS One (2016) 0.75

Genetic diversity and selection of three nuclear genes in Schistosoma japonicum populations. Parasit Vectors (2017) 0.75

3D-QSAR and Molecular Docking Studies on the TcPMCA1-Mediated Detoxification of Scopoletin and Coumarin Derivatives. Int J Mol Sci (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

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

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

An improved algorithm for matching biological sequences. J Mol Biol (1982) 21.95

I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28

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

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83

The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics (2005) 6.82

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph (1995) 6.64

Template-based modeling and free modeling by I-TASSER in CASP7. Proteins (2007) 6.45

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem (1985) 6.09

ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79

Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07

AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics (2001) 4.79

Scoring residue conservation. Proteins (2002) 4.66

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model (1997) 3.59

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54

Predicting functionally important residues from sequence conservation. Bioinformatics (2007) 3.42

How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15

Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem (2007) 3.03

Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des (2000) 2.84

3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res (2010) 2.84

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol (2009) 2.82

Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph (1992) 2.57

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44

Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics (2009) 2.42

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins (2004) 2.17

Assessment of CASP7 structure predictions for template free targets. Proteins (2007) 1.98

Assessment of CASP8 structure predictions for template free targets. Proteins (2009) 1.96

PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem Cent J (2007) 1.90

Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol (1998) 1.87

Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A (2010) 1.71

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69

LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res (2007) 1.53

Assessment of ligand-binding residue predictions in CASP9. Proteins (2011) 1.47

Binding ligand prediction for proteins using partial matching of local surface patches. Int J Mol Sci (2010) 1.23

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J Med Chem (1993) 1.22

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol (2008) 1.19

Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment. J Chem Inf Model (2010) 1.02

Protein-binding site prediction based on three-dimensional protein modeling. Proteins (2009) 0.97

Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. Proc Natl Acad Sci U S A (2011) 0.87

Articles by these authors

(truncated to the top 100)

I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66

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

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

RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72

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

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

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

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

Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24

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

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

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89

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

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

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

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

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

HAb18G (CD147), a cancer-associated biomarker and its role in cancer detection. Histopathology (2009) 1.45

Potential role of human visceral pleura in pleural fluid turnover. Chin Med J (Engl) (2006) 1.44

Infant speech perception activates Broca's area: a developmental magnetoencephalography study. Neuroreport (2006) 1.40

Toxicity and cellular responses of intestinal cells exposed to titanium dioxide. Cell Biol Toxicol (2009) 1.38

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

National survey of the medical treatment status for non-small cell lung cancer (NSCLC) in China. Lung Cancer (2012) 1.30

[Phase III randomized clinical trial of intratumoral injection of E1B gene-deleted adenovirus (H101) combined with cisplatin-based chemotherapy in treating squamous cell cancer of head and neck or esophagus]. Ai Zheng (2004) 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

Improving protein structure prediction using multiple sequence-based contact predictions. Structure (2011) 1.24

Identification of near-native structures by clustering protein docking conformations. Proteins (2007) 1.23

A protocol for computer-based protein structure and function prediction. J Vis Exp (2011) 1.23

Lipid raft redox signaling platforms in endothelial dysfunction. Antioxid Redox Signal (2007) 1.22

Deletion of the cyclic di-AMP phosphodiesterase gene (cnpB) in Mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection. Mol Microbiol (2014) 1.22

The use of quantitative real-time reverse transcriptase PCR for 5' and 3' portions of ALK transcripts to detect ALK rearrangements in lung cancers. Clin Cancer Res (2012) 1.21

TOUCHSTONE: a unified approach to protein structure prediction. Proteins (2003) 1.20

A multicenter, randomized, double-blind, placebo-controlled study to evaluate the efficacy of paclitaxel-carboplatin alone or with endostar for advanced non-small cell lung cancer. J Thorac Oncol (2011) 1.19

Uncoupling protein-2 protects endothelial function in diet-induced obese mice. Circ Res (2012) 1.19

Significance of MYCN amplification in international neuroblastoma staging system stage 1 and 2 neuroblastoma: a report from the International Neuroblastoma Risk Group database. J Clin Oncol (2008) 1.18

Lung adenocarcinomas with HER2-activating mutations are associated with distinct clinical features and HER2/EGFR copy number gains. J Thorac Oncol (2012) 1.17

Lysin motif-containing proteins LYP4 and LYP6 play dual roles in peptidoglycan and chitin perception in rice innate immunity. Plant Cell (2012) 1.16

Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16

Cyclic di-AMP impairs potassium uptake mediated by a cyclic di-AMP binding protein in Streptococcus pneumoniae. J Bacteriol (2013) 1.16

miR-1 exacerbates cardiac ischemia-reperfusion injury in mouse models. PLoS One (2012) 1.15

Comparison of exposure estimation methods for air pollutants: ambient monitoring data and regional air quality simulation. Environ Res (2012) 1.15

Genetic variants in cyclooxygenase-2: Expression and risk of gastric cancer and its precursors in a Chinese population. Gastroenterology (2006) 1.14

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Res (2009) 1.14

Mechanistic studies of Ce(IV)-mediated oxidation of beta-dicarbonyls: solvent-dependent behavior of radical cation intermediates. J Org Chem (2007) 1.14

Toward optimal fragment generations for ab initio protein structure assembly. Proteins (2012) 1.13

Frequency of well-identified oncogenic driver mutations in lung adenocarcinoma of smokers varies with histological subtypes and graduated smoking dose. Lung Cancer (2012) 1.12

iTRAQ-2DLC-ESI-MS/MS based identification of a new set of immunohistochemical biomarkers for classification of dysplastic nodules and small hepatocellular carcinoma. J Proteome Res (2011) 1.11

TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins (2003) 1.10

A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica (2006) 1.09

Corneal nerve structure and function in patients with non-sjogren dry eye: clinical correlations. Invest Ophthalmol Vis Sci (2013) 1.09

TASSER-based refinement of NMR structures. Proteins (2006) 1.09

Function of HAb18G/CD147 in invasion of host cells by severe acute respiratory syndrome coronavirus. J Infect Dis (2005) 1.09

BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins (2011) 1.08

Enhancement of autophagy by simvastatin through inhibition of Rac1-mTOR signaling pathway in coronary arterial myocytes. Cell Physiol Biochem (2013) 1.08

Analysis of major known driver mutations and prognosis in resected adenosquamous lung carcinomas. J Thorac Oncol (2014) 1.08

Bridging small-gap peripheral nerve defects using acellular nerve allograft implanted with autologous bone marrow stromal cells in primates. Brain Res (2007) 1.08

Redox regulation of NLRP3 inflammasomes: ROS as trigger or effector? Antioxid Redox Signal (2015) 1.07

Abnormal junctions and permeability of myelin in PMP22-deficient nerves. Ann Neurol (2014) 1.06

Negative Differential Resistance in ZnO Nanowires Bridging Two Metallic Electrodes. Nanoscale Res Lett (2010) 1.06

Glucagon stimulates exocytosis in mouse and rat pancreatic alpha-cells by binding to glucagon receptors. Mol Endocrinol (2004) 1.06

A theory of germinal center B cell selection, division, and exit. Cell Rep (2012) 1.06

A novel probe for the non-invasive detection of tumor-associated inflammation. Oncoimmunology (2013) 1.05

Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutant. Biochemistry (2003) 1.05

[Chemical constituents of Ligularia duciformis]. Yao Xue Xue Bao (2007) 1.05

ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One (2012) 1.05

Differential response between the p53 ubiquitin-protein ligases Pirh2 and MdM2 following DNA damage in human cancer cells. Exp Cell Res (2006) 1.04

TASSER-Lite: an automated tool for protein comparative modeling. Biophys J (2006) 1.03

Controllable synthesis of silver nanoparticle-decorated reduced graphene oxide hybrids for ammonia detection. Analyst (2013) 1.03

Modulation of CD147-induced matrix metalloproteinase activity: role of CD147 N-glycosylation. Biochem J (2013) 1.02

A comparative study on screw loosening in osteoporotic lumbar spine fusion between expandable and conventional pedicle screws. Arch Orthop Trauma Surg (2011) 1.02

Expression of TRF1, TRF2, TIN2, TERT, KU70, and BRCA1 proteins is associated with telomere shortening and may contribute to multistage carcinogenesis of gastric cancer. J Cancer Res Clin Oncol (2010) 1.02

ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. PLoS One (2008) 1.02

HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. PLoS One (2009) 1.02