Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.

PubWeight™: 1.11‹?› | Rank: Top 10%

🔗 View Article (PMC 2891173)

Published in J Chem Inf Model on March 01, 2009

Authors

Manuel Rueda1, Giovanni Bottegoni, Ruben Abagyan

Author Affiliations

1: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail TPC-28, La Jolla, California 92037, USA.

Articles citing this

Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J (2012) 1.68

GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins (2010) 1.57

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. PLoS One (2016) 1.39

Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. J Chem Theory Comput (2012) 1.18

Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17

Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci (2011) 1.09

SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci (2010) 1.01

Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One (2011) 0.99

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J (2010) 0.99

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J Comput Aided Mol Des (2012) 0.99

A flexible docking scheme to explore the binding selectivity of PDZ domains. Protein Sci (2010) 0.98

The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics (2015) 0.98

Protein flexibility in docking and surface mapping. Q Rev Biophys (2012) 0.96

ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model (2012) 0.94

Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem (2012) 0.87

Pocket-based drug design: exploring pocket space. AAPS J (2012) 0.86

Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophys J (2012) 0.86

Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures. J Chem Inf Model (2011) 0.83

Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach. J Comput Aided Mol Des (2010) 0.83

Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des (2011) 0.83

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Res (2015) 0.82

Receptor-ligand molecular docking. Biophys Rev (2013) 0.78

Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification. J Chem Inf Model (2014) 0.78

In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PLoS One (2013) 0.78

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Med Chem (2014) 0.78

Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening? PLoS One (2012) 0.75

Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target. J Mol Model (2014) 0.75

Articles cited by this

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

Essential dynamics of proteins. Proteins (1993) 11.56

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Phys Rev Lett (1996) 9.75

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41

Protein-ligand docking: current status and future challenges. Proteins (2006) 5.92

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature (2007) 5.78

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1983) 5.27

Analysis of catalytic residues in enzyme active sites. J Mol Biol (2002) 4.90

Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci U S A (1983) 4.84

Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem (2006) 4.74

Molecular dynamics and protein function. Proc Natl Acad Sci U S A (2005) 4.70

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins (2006) 3.60

Implications of protein flexibility for drug discovery. Nat Rev Drug Discov (2003) 2.83

Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83

Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol (2004) 2.65

Protein dynamics from NMR. Nat Struct Biol (2000) 2.52

Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38

Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc (2005) 2.32

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16

The role of dynamics in enzyme activity. Annu Rev Biophys Biomol Struct (2002) 2.14

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins (2007) 2.03

Normal modes as refinement parameters for the F-actin model. Biophys J (1995) 1.86

Accommodating protein flexibility in computational drug design. Mol Pharmacol (2000) 1.84

Dynamics of different functional parts of bacteriorhodopsin: H-2H labeling and neutron scattering. Proc Natl Acad Sci U S A (1998) 1.81

Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74

A consensus view of protein dynamics. Proc Natl Acad Sci U S A (2007) 1.73

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J Mol Biol (1999) 1.68

Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol (2004) 1.56

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins (1995) 1.54

Normal mode analysis of G-actin. J Mol Biol (1993) 1.52

Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc (2007) 1.52

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis. Protein Sci (1994) 1.51

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem (2005) 1.50

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophys J (2006) 1.45

Docking essential dynamics eigenstructures. Proteins (2005) 1.45

Flexible docking in solution using metadynamics. J Am Chem Soc (2005) 1.43

Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des (2003) 1.39

Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng (2003) 1.36

Fully automated molecular mechanics based induced fit protein-ligand docking method. J Chem Inf Model (2008) 1.34

Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Proc Natl Acad Sci U S A (2008) 1.34

Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol (1994) 1.30

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results. J Comput Aided Mol Des (2008) 1.25

Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure (2007) 1.24

Predictions of protein flexibility: first-order measures. Proteins (2004) 1.21

Molecular dynamics of biological macromolecules: a brief history and perspective. Biopolymers (2003) 1.17

Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J Am Chem Soc (2004) 1.15

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem (2008) 1.12

Normal modes and essential dynamics. Methods Mol Biol (2008) 1.12

Locating the active sites of enzymes using mechanical properties. Proteins (2007) 1.07

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07

Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Protein Sci (2008) 1.05

Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3beta inhibitors. J Med Chem (2005) 0.99

Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors. FEBS Lett (2006) 0.96

Structure selection for protein kinase docking and virtual screening: homology models or crystal structures? Curr Protein Pept Sci (2006) 0.94

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase. J Chem Inf Model (2006) 0.94

Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations. Proteins (2004) 0.93

Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins (2004) 0.92

Exploring the Essential Dynamics of B-DNA. J Chem Theory Comput (2005) 0.89

Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulations. ChemMedChem (2007) 0.88

Protein structures in virtual screening: a case study with CDK2. J Med Chem (2006) 0.86

Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family. J Med Chem (2007) 0.85

Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. J Mol Graph Model (2007) 0.83

The effect of multiple binding modes on empirical modeling of ligand docking to proteins. Protein Sci (1999) 0.76

Articles by these authors

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30

METLIN: a metabolite mass spectral database. Ther Drug Monit (2005) 10.15

Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science (2007) 5.49

Structure of the human histamine H1 receptor complex with doxepin. Nature (2011) 3.48

Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol (2010) 3.38

Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29

Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83

Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc (2010) 2.62

Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (2011) 2.11

Nuclear hormone receptor targeted virtual screening. J Med Chem (2003) 2.05

Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J Mol Recognit (2009) 2.05

Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem (2010) 1.88

Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol (2004) 1.79

The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol (2006) 1.70

Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins (2005) 1.69

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics (2006) 1.68

Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65

ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins (2003) 1.63

Soft protein-protein docking in internal coordinates. Protein Sci (2002) 1.60

GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins (2010) 1.57

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics (2002) 1.56

Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci (2006) 1.55

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A (2003) 1.53

Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (2002) 1.52

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov (2012) 1.50

A catalytically silent FAAH-1 variant drives anandamide transport in neurons. Nat Neurosci (2011) 1.50

Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des (2009) 1.48

Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42

Diaryl Urea: A Privileged Structure in Anticancer Agents. Curr Med Chem (2016) 1.40

Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem (2008) 1.38

Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des (2012) 1.34

Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology (2010) 1.31

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins (2006) 1.29

Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. J Med Chem (2009) 1.28

A new method for publishing three-dimensional content. PLoS One (2009) 1.23

Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. J Biol Chem (2011) 1.22

PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22

Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21

Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem (2007) 1.21

Predictions of protein flexibility: first-order measures. Proteins (2004) 1.21

Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal (2011) 1.20

3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A (2007) 1.20

Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17

Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol (2007) 1.16

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol (2002) 1.14

Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem Int Ed Engl (2010) 1.13

Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J (2012) 1.13

Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Mol Pharmacol (2009) 1.12

Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology (2010) 1.10

FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (2009) 1.09

Defining the CD59-C9 binding interaction. J Biol Chem (2006) 1.09

Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell (2013) 1.07

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07

A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl (2012) 1.06

Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding. Mol Pharmacol (2008) 1.06

Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem (2011) 1.06

Small molecule aurora kinases inhibitors. Curr Med Chem (2009) 1.06

Determinants of retinoid X receptor transcriptional antagonism. J Med Chem (2004) 1.05

SGC--structural biology and human health: a new approach to publishing structural biology results. PLoS One (2009) 1.02

Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure (2011) 1.01

Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment. J Biol Chem (2010) 1.01

Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. J Med Chem (2010) 1.00

Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One (2011) 0.99

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. J Chem Inf Model (2011) 0.99

ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem (2003) 0.99

Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem (2007) 0.98

Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins (2005) 0.97

Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One (2013) 0.96

The transthyretin-related protein family. Eur J Biochem (2003) 0.96

Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J Biol Chem (2007) 0.96

Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett (2004) 0.95

ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model (2012) 0.94

Ligand-guided receptor optimization. Methods Mol Biol (2012) 0.94

Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem (2005) 0.94

GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci (2011) 0.93

Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol (2013) 0.93

Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem (2012) 0.93

Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol (2012) 0.92

Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochem Biophys Res Commun (2007) 0.92

Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. J Biol Chem (2012) 0.92

Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel (2003) 0.92

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des (2010) 0.92

Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B (2012) 0.91

Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model (2008) 0.91

Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem (2005) 0.91

Molecular modeling and mutagenesis of gap junction channels. Prog Biophys Mol Biol (2007) 0.90

In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol (2014) 0.90

REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics (2005) 0.90

Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol (2005) 0.90

Damped-dynamics flexible fitting. Biophys J (2008) 0.89

Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction. Biochemistry (2007) 0.89

Combining galantamine and memantine in multitargeted, new chemical entities potentially useful in Alzheimer's disease. J Med Chem (2012) 0.88

A natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb) (2011) 0.88

Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem (2013) 0.87

Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. Anal Chem (2006) 0.87