Latest developments in molecular docking: 2010-2011 in review (Q38092807)

28 August 2017

Latest developments in molecular docking: 2010-2011 in review (English)

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28 August 2017

Elizabeth Yuriev

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Paul A. Ramsland

object named as

Paul A Ramsland

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2

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publication date

1 May 2013

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Journal of Molecular Recognition

28 August 2017

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28 August 2017

26

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28 August 2017

215-239

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28 August 2017

5

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A collaborative filtering approach for protein-protein docking scoring functions

28 August 2017

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Recent insights on the medicinal chemistry of metal-based compounds: hints for the successful drug design.

21 January 2018

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Challenges and advances in computational docking: 2009 in review

21 January 2018

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Toward a robust search method for the protein-drug docking problem.

21 January 2018

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A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors

21 January 2018

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A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity.

21 January 2018

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BetaDock: shape-priority docking method based on beta-complex.

21 January 2018

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LigDockCSA: protein-ligand docking using conformational space annealing.

21 January 2018

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Fast docking using the CHARMM force field with EADock DSS.

21 January 2018

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Theory of docking scores and its application to a customizable scoring function

21 January 2018

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SKATE: a docking program that decouples systematic sampling from scoring

21 January 2018

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A python-based docking program utilizing a receptor bound ligand shape: PythDock.

21 January 2018

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VoteDock: consensus docking method for prediction of protein-ligand interactions

21 January 2018

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Rapid flexible docking using a stochastic rotamer library of ligands

21 January 2018

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ParaDockS: a framework for molecular docking with population-based metaheuristics

21 January 2018

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Efficient incorporation of protein flexibility and dynamics into molecular docking simulations

21 January 2018

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Accounting for induced-fit effects in docking: what is possible and what is not?

21 January 2018

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Automated docking with grid-based energy evaluation

21 January 2018

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Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments.

21 January 2018

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Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

21 January 2018

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Recipes for the selection of experimental protein conformations for virtual screening

21 January 2018

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ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

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Systematic exploitation of multiple receptor conformations for virtual ligand screening

21 January 2018

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Improved protein-ligand docking using GOLD

21 January 2018

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The ensemble performance index: an improved measure for assessing ensemble pose prediction performance.

21 January 2018

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Chemical space sampling by different scoring functions and crystal structures.

21 January 2018

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Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures

21 January 2018

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Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

21 January 2018

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Ensemble Docking from Homology Models.

21 January 2018

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How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

21 January 2018

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Predictive power of molecular dynamics receptor structures in virtual screening

21 January 2018

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Mining flexible-receptor docking experiments to select promising protein receptor snapshots

21 January 2018

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FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection.

21 January 2018

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Significant enhancement of docking sensitivity using implicit ligand sampling

21 January 2018

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Ligand-steered modeling and docking: A benchmarking study in class A G-protein-coupled receptors

21 January 2018

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Docking-based virtual screening for ligands of G protein-coupled receptors: not only crystal structures but also in silico models.

21 January 2018

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Homology modeling and docking evaluation of aminergic G protein-coupled receptors

21 January 2018

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Structure based prediction of subtype-selectivity for adenosine receptor antagonists

21 January 2018

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GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex

21 January 2018

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Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

21 January 2018

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Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target

21 January 2018

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DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.

21 January 2018

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Efficient inclusion of receptor flexibility in grid-based protein-ligand docking.

21 January 2018

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Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

21 January 2018

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Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

21 January 2018

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Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

21 January 2018

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Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions

21 January 2018

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Virtual screening using molecular simulations

21 January 2018

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Ligand-protein cross-docking with water molecules

21 January 2018

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Role of water in molecular docking simulations of cytochrome P450 2D6.

21 January 2018

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A fast flexible docking method using an incremental construction algorithm.

21 January 2018

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Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site

21 January 2018

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Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.

21 January 2018

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Molecular docking with ligand attached water molecules.

21 January 2018

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Comparative evaluation of 11 scoring functions for molecular docking

21 January 2018

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A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

21 January 2018

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Assessment of a novel scoring method based on solvent accessible surface area descriptors

21 January 2018

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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

21 January 2018

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Rapid context-dependent ligand desolvation in molecular docking

21 January 2018

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Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations

21 January 2018

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Postprocessing of protein-ligand docking poses using linear response MM-PB/SA: application to Wee1 kinase inhibitors

21 January 2018

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Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions

21 January 2018

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Postprocessing of docked protein-ligand complexes using implicit solvation models.

21 January 2018

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A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

21 January 2018

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Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

21 January 2018

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Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

21 January 2018

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Statistical potential for modeling and ranking of protein-ligand interactions

21 January 2018

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An interaction-motif-based scoring function for protein-ligand docking

21 January 2018

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A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

21 January 2018

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Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions.

21 January 2018

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Prediction of protein-ligand binding affinities using multiple instance learning.

21 January 2018

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PLS-DA - Docking Optimized Combined Energetic Terms (PLSDA-DOCET) protocol: a brief evaluation.

21 January 2018

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FRED pose prediction and virtual screening accuracy

21 January 2018

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Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets

21 January 2018

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Consensus virtual screening approaches to predict protein ligands.

21 January 2018

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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

21 January 2018

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NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes

21 January 2018

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NNScore 2.0: a neural-network receptor-ligand scoring function

21 January 2018

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A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

21 January 2018

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A machine learning-based method to improve docking scoring functions and its application to drug repurposing

21 January 2018

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Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening.

21 January 2018

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Prediction of ligand binding using an approach designed to accommodate diversity in protein-ligand interactions

21 January 2018

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Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets.

21 January 2018

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Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries

21 January 2018

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Target-specific support vector machine scoring in structure-based virtual screening: computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation

21 January 2018

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PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements

21 January 2018

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Robust scoring functions for protein-ligand interactions with quantum chemical charge models

21 January 2018

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High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors

21 January 2018

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Knowledge-based scoring functions in drug design. 1. Developing a target-specific method for kinase-ligand interactions.

21 January 2018

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Comparative binding energy analysis for binding affinity and target selectivity prediction

21 January 2018

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eHiTS: an innovative approach to the docking and scoring function problems.

21 January 2018

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Improving molecular docking through eHiTS' tunable scoring function.

21 January 2018

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Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction

21 January 2018

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In silico fragment-based drug design

21 January 2018

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Docking performance of fragments and druglike compounds.

21 January 2018

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SERAPhiC: a benchmark for in silico fragment-based drug design.

21 January 2018

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Binding-site assessment by virtual fragment screening

21 January 2018

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Using protein-ligand docking to assess the chemical tractability of inhibiting a protein target.

21 January 2018

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Structure-based fragment hopping for lead optimization using predocked fragment database

21 January 2018

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Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition

21 January 2018

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Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor

21 January 2018

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Structure-Based Approaches to Target Fishing and Ligand Profiling

21 January 2018

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An inverse docking approach for identifying new potential anti-cancer targets.

21 January 2018

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A comparative reverse docking strategy to identify potential antineoplastic targets of tea functional components and binding mode

21 January 2018

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Improving performance of docking-based virtual screening by structural filtration.

21 January 2018

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Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR.

21 January 2018

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A computational approach for exploring carbohydrate recognition by lectins in innate immunity

21 January 2018

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Antibody recognition of cancer-related gangliosides and their mimics investigated using in silico site mapping

21 January 2018

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In silico analysis of antibody-carbohydrate interactions and its application to xenoreactive antibodies

21 January 2018

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Automatic clustering of docking poses in virtual screening process using self-organizing map.

21 January 2018

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MiniMuDS: a new optimizer using knowledge-based potentials improves scoring of docking solutions.

21 January 2018

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Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons

21 January 2018

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Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies

21 January 2018

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An Improved Weighted-Residue Profile Based Method of Using Protein-Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists

21 January 2018

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Drug efficiency indices for improvement of molecular docking scoring functions.

21 January 2018

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Using free energy of binding calculations to improve the accuracy of virtual screening predictions

21 January 2018

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Homology models in docking and high-throughput docking.

21 January 2018

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Predicting the accuracy of protein-ligand docking on homology models.

21 January 2018

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Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?

21 January 2018

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Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride

21 January 2018

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Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

21 January 2018

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Discovery of Novel α4β2 Neuronal Nicotinic Receptor Modulators through Structure-Based Virtual Screening

21 January 2018

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Pharmacological validation of Trypanosoma brucei phosphodiesterases B1 and B2 as druggable targets for African sleeping sickness

21 January 2018

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Molecular docking and competitive binding study discovered different binding modes of microsomal prostaglandin E synthase-1 inhibitors

21 January 2018

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New aryl hydrocarbon receptor homology model targeted to improve docking reliability

21 January 2018

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Homology Model and Docking-Based Virtual Screening for Ligands of the σ1 Receptor.

21 January 2018

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Molecular modeling: a search for a calpain inhibitor as a new treatment for cataractogenesis

21 January 2018

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Identification of inhibitors against p90 ribosomal S6 kinase 2 (RSK2) through structure-based virtual screening with the inhibitor-constrained refined homology model.

21 January 2018

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Identification of novel inhibitors of tropomyosin-related kinase A through the structure-based virtual screening with homology-modeled protein structure

21 January 2018

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Protein kinases: docking and homology modeling reliability.

21 January 2018

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Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening

21 January 2018

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Structure-based prediction of subtype selectivity of histamine H3 receptor selective antagonists in clinical trials

21 January 2018

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The 5-HT(1A) agonism potential of substituted piperazine-ethyl-amide derivatives is conserved in the hexyl homologues: molecular modeling and pharmacological evaluation.

21 January 2018

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Affinity of aporphines for the human 5-HT2A receptor: insights from homology modeling and molecular docking studies

21 January 2018

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X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery

21 January 2018

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Docking validation resources: protein family and ligand flexibility experiments

21 January 2018

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DOCK 6: combining techniques to model RNA-small molecule complexes

21 January 2018

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Structure-based virtual screening of glycogen synthase kinase 3β inhibitors: analysis of scoring functions applied to large true actives and decoy sets.

21 January 2018

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Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists

21 January 2018

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Structure-based discovery of A2A adenosine receptor ligands

21 January 2018

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Ligand discovery from a dopamine D3 receptor homology model and crystal structure

21 January 2018

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Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore

21 January 2018

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Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling

21 January 2018

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Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment

21 January 2018

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Quo vadis, virtual screening? A comprehensive survey of prospective applications

21 January 2018

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Identification of novel urease inhibitors by high-throughput virtual and in vitro screening

21 January 2018

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Virtual decoy sets for molecular docking benchmarks.

21 January 2018

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Normalizing molecular docking rankings using virtually generated decoys

21 January 2018

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DEKOIS: demanding evaluation kits for objective in silico screening--a versatile tool for benchmarking docking programs and scoring functions

21 January 2018

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Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.

21 January 2018

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Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers.

21 January 2018

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MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

21 January 2018

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VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.

21 January 2018

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Multilevel Parallelization of AutoDock 4.2.

21 January 2018

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Accelerating molecular docking calculations using graphics processing units.

21 January 2018

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GPU acceleration of Dock6's Amber scoring computation.

21 January 2018

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Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening.

21 January 2018

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Biased retrieval of chemical series in receptor-based virtual screening.

21 January 2018

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A unified, probabilistic framework for structure- and ligand-based virtual screening.

21 January 2018

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Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors.

21 January 2018

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CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

21 January 2018

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Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction

21 January 2018

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CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

21 January 2018

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Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function

21 January 2018

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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

21 January 2018

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Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes.

21 January 2018

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Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment.

21 January 2018

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Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors

21 January 2018

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Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase

21 January 2018

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A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors

21 January 2018

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AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors

21 January 2018

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CrystalDock: a novel approach to fragment-based drug design

21 January 2018

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AUDocker LE: A GUI for virtual screening with AUTODOCK Vina

21 January 2018

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Dockomatic - automated ligand creation and docking

21 January 2018

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DockoMatic: automated peptide analog creation for high throughput virtual screening

21 January 2018

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iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis

21 January 2018

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Ligand docking and binding site analysis with PyMOL and Autodock/Vina

21 January 2018

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VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform

21 January 2018

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iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

21 January 2018

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SwissDock, a protein-small molecule docking web service based on EADock DSS

21 January 2018

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A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

21 January 2018

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VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface

21 January 2018

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Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in CytochromecPeroxidase

21 January 2018

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Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/JMR.2266

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28 August 2017

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PubMed ID

23526775