Tópico 9

Palavras

bind ( 1733 )
structur ( 1185 )
ligand ( 1036 )
protein ( 1010 )
site ( 938 )
interact ( 933 )
energi ( 913 )
dock ( 893 )
molecular ( 836 )
conform ( 669 )
receptor ( 590 )
inhibitor ( 522 )
complex ( 518 )
free ( 500 )
predict ( 488 )
affin ( 472 )
target ( 453 )
molecul ( 443 )
score ( 415 )
dynam ( 407 )
residu ( 406 )
function ( 394 )
simul ( 349 )
calcul ( 342 )
pose ( 294 )
enzym ( 286 )
experiment ( 247 )
activ ( 243 )
mode ( 240 )
flexibl ( 234 )
atom ( 229 )
stabil ( 191 )
design ( 168 )
inhibit ( 143 )
mechan ( 141 )
bound ( 141 )
acid ( 139 )
fragment ( 130 )
rank ( 129 )
known ( 127 )
reveal ( 117 )
contribut ( 117 )
domain ( 112 )
form ( 109 )
properti ( 108 )
ensembl ( 95 )
channel ( 89 )
small ( 87 )
chain ( 86 )
surfac ( 78 )
xray ( 76 )
conserv ( 76 )
seri ( 71 )
favor ( 71 )
protocol ( 66 )
fold ( 63 )
benchmark ( 62 )
correl ( 61 )
upon ( 59 )
reproduc ( 58 )
divers ( 58 )
success ( 51 )
entropi ( 51 )
select ( 46 )
toward ( 45 )
explicit ( 44 )
modif ( 43 )
exhibit ( 43 )
famili ( 40 )
threedimension ( 37 )
orient ( 36 )
attract ( 33 )
geometri ( 29 )
close ( 29 )
classic ( 26 )
refin ( 25 )
induc ( 25 )
insight ( 20 )
weak ( 19 )
top ( 18 )
carri ( 18 )
wide ( 17 )
suggest ( 14 )
basi ( 14 )
coordin ( 14 )
rapid ( 13 )
absenc ( 13 )
align ( 13 )
contain ( 13 )
accuraci ( 12 )
competit ( 12 )
consider ( 12 )
multipl ( 11 )
start ( 10 )
trajectori ( 10 )
led ( 10 )
compris ( 10 )
synthes ( 9 )
rather ( 9 )
togeth ( 8 )

Resumos

J Chem Inf Model - Develop and test a solvent accessible surface area-based model in conformational entropy calculations. ( 77 )
J Chem Inf Model - Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies. ( 65 )
J Chem Inf Model - PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. ( 64 )
J Chem Inf Model - Statistical potential for modeling and ranking of protein-ligand interactions. ( 62 )
J Chem Inf Model - Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. ( 58 )
J Chem Inf Model - Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations. ( 57 )
J Chem Inf Model - Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA. ( 57 )
J Chem Inf Model - Postprocessing of docked protein-ligand complexes using implicit solvation models. ( 56 )
J Chem Inf Model - Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. ( 55 )
J Chem Inf Model - Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols. ( 55 )
J Chem Inf Model - Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules. ( 54 )
J Chem Inf Model - Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. ( 51 )
J Chem Inf Model - Dynamics of noncovalent interactions in all-a and all-? class proteins: implications for the stability of amyloid aggregates. ( 50 )
J Chem Inf Model - Multiple interaction regions in the orthosteric ligand binding domain of the a7 neuronal nicotinic acetylcholine receptor. ( 50 )
J Chem Inf Model - Binding conformation of 2-oxoamide inhibitors to group IVA cytosolic phospholipase A2 determined by molecular docking combined with molecular dynamics. ( 50 )
J Chem Inf Model - Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. ( 49 )
J Chem Inf Model - Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors. ( 49 )
J Chem Inf Model - Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results. ( 49 )
J Chem Inf Model - Computational study on the drug resistance mechanism against HCV NS3/4A protease inhibitors vaniprevir and MK-5172 by the combination use of molecular dynamics simulation, residue interaction network, and substrate envelope analysis. ( 48 )
J Chem Inf Model - Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors. ( 48 )
J Chem Inf Model - Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark. ( 48 )
J Chem Inf Model - Computational method to identify druggable binding sites that target protein-protein interactions. ( 47 )
J Chem Inf Model - Significant enhancement of docking sensitivity using implicit ligand sampling. ( 47 )
J Chem Inf Model - Profiling the structural determinants for the selectivity of representative factor-Xa and thrombin inhibitors using combined ligand-based and structure-based approaches. ( 46 )
J Chem Inf Model - Ligand-receptor affinities computed by an adapted linear interaction model for continuum electrostatics and by protein conformational averaging. ( 45 )
J Chem Inf Model - Structure-based multiscale approach for identification of interaction partners of PDZ domains. ( 45 )
J Chem Inf Model - AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors. ( 45 )
J Chem Inf Model - Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. ( 44 )
J Chem Inf Model - A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study. ( 44 )
J Chem Inf Model - Docking challenge: protein sampling and molecular docking performance. ( 44 )
J Chem Inf Model - Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions. ( 44 )
J Chem Inf Model - Structure-based and multiple potential three-dimensional quantitative structure-activity relationship (SB-MP-3D-QSAR) for inhibitor design. ( 43 )
J Chem Inf Model - Predicting fragment binding poses using a combined MCSS MM-GBSA approach. ( 43 )
J Chem Inf Model - Rigorous treatment of multispecies multimode ligand-receptor interactions in 3D-QSAR: CoMFA analysis of thyroxine analogs binding to transthyretin. ( 42 )
J Chem Inf Model - Intrinsic energy landscapes of amino acid side-chains. ( 42 )
J Chem Inf Model - BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. ( 42 )
J Chem Inf Model - Structural properties of non-traditional drug targets present new challenges for virtual screening. ( 42 )
J Chem Inf Model - Subtype selectivity of dopamine receptor ligands: insights from structure and ligand-based methods. ( 42 )
J Chem Inf Model - Ligand binding site identification by higher dimension molecular dynamics. ( 42 )
J Chem Inf Model - Investigation on the effect of key water molecules on docking performance in CSARdock exercise. ( 41 )
J Chem Inf Model - Global free energy scoring functions based on distance-dependent atom-type pair descriptors. ( 41 )
J Chem Inf Model - Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification. ( 41 )
J Chem Inf Model - DOLINA--docking based on a local induced-fit algorithm: application toward small-molecule binding to nuclear receptors. ( 41 )
J Chem Inf Model - Novel inhibitor discovery through virtual screening against multiple protein conformations generated via ligand-directed modeling: a maternal embryonic leucine zipper kinase example. ( 41 )
J Chem Inf Model - Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with p38a MAP kinase. ( 40 )
J Chem Inf Model - A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. ( 40 )
J Chem Inf Model - Molecular docking and competitive binding study discovered different binding modes of microsomal prostaglandin E synthase-1 inhibitors. ( 40 )
J Chem Inf Model - Using free energy of binding calculations to improve the accuracy of virtual screening predictions. ( 40 )
J Chem Inf Model - Ensemble-based docking using biased molecular dynamics. ( 40 )
J Chem Inf Model - Unraveling the allosteric inhibition mechanism of PTP1B by free energy calculation based on umbrella sampling. ( 39 )
J Chem Inf Model - Influence of protonation on substrate and inhibitor interactions at the active site of human monoamine oxidase-A. ( 39 )
J Chem Inf Model - A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. ( 39 )
J Chem Inf Model - Including explicit water molecules as part of the protein structure in MM/PBSA calculations. ( 39 )
J Chem Inf Model - Addressing selective polypharmacology of antipsychotic drugs targeting the bioaminergic receptors through receptor dynamic conformational ensembles. ( 38 )
J Chem Inf Model - Ligand aligning method for molecular docking: alignment of property-weighted vectors. ( 38 )
J Chem Inf Model - Modeling, molecular dynamics simulation, and mutation validation for structure of cannabinoid receptor 2 based on known crystal structures of GPCRs. ( 38 )
J Chem Inf Model - Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations. ( 38 )
J Chem Inf Model - Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines. ( 38 )
J Chem Inf Model - Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. ( 38 )
J Chem Inf Model - Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. ( 38 )
J Chem Inf Model - Conformational free energy modeling of druglike molecules by metadynamics in the WHIM space. ( 38 )
J Chem Inf Model - Computational modeling of the catalytic mechanism of human placental alkaline phosphatase (PLAP). ( 38 )
Comput Biol Chem - Affinity of HIV-1 antibody 2G12 with monosaccharides: a theoretical study based on explicit and implicit water models. ( 37 )
J Chem Inf Model - LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles. ( 37 )
J Chem Inf Model - Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation. ( 37 )
J Chem Inf Model - Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations. ( 37 )
J Chem Inf Model - Elucidation of conformational states, dynamics, and mechanism of binding in human -opioid receptor complexes. ( 37 )
J Chem Inf Model - Molecular determinants of binding to the Plasmodium subtilisin-like protease 1. ( 37 )
J Chem Inf Model - Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. ( 36 )
J Chem Inf Model - Molecular dynamic behavior and binding affinity of flavonoid analogues to the cyclin dependent kinase 6/cyclin D complex. ( 36 )
J Chem Inf Model - Thermodynamics of fragment binding. ( 36 )
J Chem Inf Model - A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations. ( 36 )
J Chem Inf Model - Elucidating a key component of cancer metastasis: CXCL12 (SDF-1a) binding to CXCR4. ( 36 )
J Chem Inf Model - Docking validation resources: protein family and ligand flexibility experiments. ( 36 )
J Chem Inf Model - Structural insight into the unique binding properties of pyridylethanol(phenylethyl)amine inhibitor in human CYP51. ( 36 )
J Chem Inf Model - Accounting for target flexibility and water molecules by docking to ensembles of target structures: the HCV NS5B palm site I inhibitors case study. ( 36 )
J Chem Inf Model - Ligand Identification Scoring Algorithm (LISA). ( 36 )
J Chem Inf Model - Residue preference mapping of ligand fragments in the Protein Data Bank. ( 36 )
J Chem Inf Model - Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs. ( 36 )
J Chem Inf Model - In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE. ( 36 )
J Chem Inf Model - Experimentally guided structural modeling and dynamics analysis of Hsp90-p53 interactions: allosteric regulation of the Hsp90 chaperone by a client protein. ( 36 )
Comput. Biol. Med. - A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach. ( 35 )
J Chem Inf Model - Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design. ( 35 )
J Chem Inf Model - GalaxyDock: protein-ligand docking with flexible protein side-chains. ( 35 )
J Chem Inf Model - AcquaAlta: a directional approach to the solvation of ligand-protein complexes. ( 35 )
J Chem Inf Model - Structural modeling of HCV NS3/4A serine protease drug-resistance mutations using end-point continuum solvation and side-chain flexibility calculations. ( 35 )
J Chem Inf Model - A machine learning-based method to improve docking scoring functions and its application to drug repurposing. ( 35 )
J Chem Inf Model - Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set. ( 35 )
J Chem Inf Model - Docking server for the identification of heparin binding sites on proteins. ( 35 )
J Chem Inf Model - Data mining of supersecondary structure homology between light chains of immunogloblins and MHC molecules: absence of the common conformational fragment in the human IgM rheumatoid factor. ( 34 )
J Chem Inf Model - Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. ( 34 )
J Chem Inf Model - Analysis of factors influencing hydration site prediction based on molecular dynamics simulations. ( 34 )
J Chem Inf Model - Beware of machine learning-based scoring functions-on the danger of developing black boxes. ( 34 )
J Chem Inf Model - Characterizing the dynamics and ligand-specific interactions in the human leukocyte elastase through molecular dynamics simulations. ( 34 )
J Chem Inf Model - Binding selectivity studies of phosphoinositide 3-kinases using free energy calculations. ( 34 )
J Chem Inf Model - Interference of boswellic acids with the ligand binding domain of the glucocorticoid receptor. ( 34 )
J Chem Inf Model - Knowledge-based scoring functions in drug design: 2. Can the knowledge base be enriched? ( 33 )
J Chem Inf Model - Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity? ( 33 )
J Chem Inf Model - Functional motions modulating VanA ligand binding unraveled by self-organizing maps. ( 33 )
J Chem Inf Model - Docking studies on DNA intercalators. ( 33 )