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Ensemble docking revisited
2010
Journal of Cheminformatics
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Our protein-ligand docking approach GOLD [1,2] has been extended to search such conformational ensembles time-efficiently. ...
In recent years, the importance of considering induced fit effects in molecular docking calculations has been widely recognised in the molecular modelling community. ...
Our protein-ligand docking approach GOLD [1, 2] has been extended to search such conformational ensembles time-efficiently. ...
doi:10.1186/1758-2946-2-s1-p25
pmcid:PMC2867158
fatcat:5t5x7rqcqbbc3mqkwksbhwzvku
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
2017
Journal of Computer-Aided Molecular Design
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We used those structures to revisit our docking protocol and identify the major limiting factor for our docking performance in Stage1. ...
the major cluster were additionally included in the docking ensemble, until the ensemble size reached the maximum of 10. ...
doi:10.1007/s10822-017-0049-y
pmid:28831657
pmcid:PMC5767195
fatcat:5yvgxm64ajfnheop4e2ogppbci
Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design
2012
Chemical Biology and Drug Design
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We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques ...
See Figure 2 for a schematic of ensemble-based docking methods. ...
Ensemble-Based Screening Methods Ensemble-based screening methods rely on using varied receptor conformations in a docking protocol. ...
doi:10.1111/cbdd.12051
pmid:23253130
pmcid:PMC3540989
fatcat:tso4kv2zqrfmndvfkekcw3f24a
Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement
2016
Physical Chemistry, Chemical Physics - PCCP
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The effect of spin label mobility on the accuracy of protein–protein docking calculations was investigated using inter- and intra-molecular PRE data. ...
Position
SL conformer ensemble The protein docking calculations were repeated using the same inter-molecular PRE data and an ensemble of four SL conformers. ...
As was shown previously, 14 fixing the SL orientations during docking produces a highly defined ensemble of solutions. ...
doi:10.1039/c5cp03781f
pmid:26356049
fatcat:ufq2ewtqoja7lexmrdvnpf4tnu
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies
[article]
2020
bioRxiv
pre-print
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Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. ...
Similarly, the ensemble of BTK+binder docked against cereblon+binder in Case Study 4 was generated once, and then copies of this protein-protein docked ensemble were used in multiple independent simulations ...
The protein-protein docked ensembles built with Method 4B were also reused for Method 5. ...
doi:10.1101/2020.07.10.197186
fatcat:clrhjxtrkjgk5a5bm2w3d5glty
Generative Topographic Mapping of the Docking Conformational Space
2019
Molecules
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Then, projection of poses of other ligands on such landscapes might serve to predict those falling in native zones as being well-docked. (2) Distinguish ligands–characterized by their ensemble of conformers–by ...
Moreover, the intuitive visualization and analysis of docking CS may, as already mentioned, have several applications–from highlighting of key contacts to monitoring docking calculation convergence. ...
Aligned landscapes of the CF map, on which the docked ensemble of conformers of 1CKP was projected. ...
doi:10.3390/molecules24122269
fatcat:xvng74rkazfgnjfvuexu5f54rm
Protein-ligand docking: Current status and future challenges
2006
Proteins: Structure, Function, and Bioinformatics
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Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. ...
Protein-ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. ...
an example of an ensemble docking method. ...
doi:10.1002/prot.21082
pmid:16862531
fatcat:iprk2g6avvfo3migaay7dfgu24
Protein social behavior makes a stronger signal for partner identification than surface geometry
2016
Proteins: Structure, Function, and Bioinformatics
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Simulation (Equip@Meso project -ANR-10-EQPX-29-01, Excellence Program "Investissement d'Avenir"); the World Community Grid (WCG,www.worldcommunitygrid.org) and WCG volunteers that allowed us to perform cross-docking ...
only a tiny fraction of the ensemble of docking models actually generated. ...
conformational ensemble. ...
doi:10.1002/prot.25206
pmid:27802579
pmcid:PMC5242317
fatcat:6bo4kklarfbotklzh7tshj7uxa
Recent Estimates of the Structure of the Factor VIIa (FVIIa)/Tissue Factor (TF) and Factor Xa (FXa) Ternary Complex
2010
Thrombosis Research
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Two independently derived docking models proposed in 2003 (one for our laboratory: CHeA and one from the Scripps laboratory: Ss) are dynamically equilibrated for over 10 ns in an electrically neutral solution ...
Thus we wished to revisit these two models and provide a more extensive, current "best-guess" solution-equilibrated model. ...
as opposed to protein-rigid docking without dynamics [16] . ...
doi:10.1016/j.thromres.2010.01.022
pmid:20156644
pmcid:PMC2839023
fatcat:463oqlxu6nd2tgc47na2uvbw3y
Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking
2009
Proteins: Structure, Function, and Bioinformatics
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While docking with the ensemble of the ten low-scoring RosettaAntibody models, to allow an average of 1000 docking models corresponding to each conformer in the ensemble, 10,000 docking models are generated ...
In cases presented here, using the ten top-scoring models was sufficient to significantly improve docking accuracy through ensemble docking. ...
doi:10.1002/prot.22309
pmid:19062174
pmcid:PMC2909601
fatcat:rxgs2dch65cnvgh7txe3oohuqi
Identification of Pharmacological Targets Combining Docking and Molecular Dynamics Simulations
2013
American Journal of Agricultural and Biological Science
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Additionally, MD simulations can depict several binding sites of ligands that can be explored by docking studies, sampling many protein conformations. ...
In this review, the most frequent criteria that are considered when determining pharmacological targets are gathered, particularly when docking and MD are combined. ...
The combination of REMD generalized ensemble sampling with ensemble docking and free energy pathway analysis has been recently proposed as a novel research protocol for the simulation of protein-ligand ...
doi:10.3844/ajabssp.2013.89.106
fatcat:32iusmg7jjehrp3uu7vnl6idl4
Multiple native states reveal persistent ruggedness of an RNA folding landscape
2010
Nature
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In the second step, the P1 duplex docks into tertiary interactions in the active site 20,21 . ...
If all Figure 1 | Docking and cleavage of the oligonucleotide substrate by the Tetrahymena ribozyme, observed using single-molecule FRET. ...
These observations prompt us to revisit the Levinthal paradox in a different context. ...
doi:10.1038/nature08717
pmid:20130651
pmcid:PMC2818749
fatcat:h5boltuj2zgcnc4cghnvpujf7i
Past, Present, and Future of Molecular Docking
[chapter]
2020
Drug Discovery and Development - New Advances [Working Title]
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The present goals, such as molecular flexibility, binding entropy, and the presence of ions and solute conditions, are revisited with the purpose of anticipating the challenges, goals, and achievements ...
This chapter presents a broad plethora of possibilities arising from the old docking alternatives to the current software technology and critically dissects and discusses the emerging trends. ...
Docking ensembles using rigid proteins can be slightly inaccurate. ...
doi:10.5772/intechopen.90921
fatcat:4ysv7rhfvjhfnlaomuag5ltkri
Recognition of the HIV Capsid by the TRIM5α Restriction Factor Is Mediated by a Subset of Pre-Existing Conformations of the TRIM5α SPRY Domain
2014
Biochemistry
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The docking of the SPRY conformations representing 10 most populated states onto the high-resolution model of the assembled HIV-1 capsid revealed that a subset of v1 conformations produced plausible binding ...
Computational protein-protein docking provides an unbiased approach for scoring, sorting, and identifying most compatible structures from an ensemble of conformations. ...
Furthemore, analysis of conformations in the most populated clusters reveals that these energetic basins were revisited multiple times along the trajectory (Supporting Information Figure S4d ), another ...
doi:10.1021/bi4014962
pmid:24506064
pmcid:PMC4119003
fatcat:igsn5nppgvcn3j76igqjxqleim
Using Smart Cameras to Localize Self-Assembling Modular Robots
2007
2007 First ACM/IEEE International Conference on Distributed Smart Cameras
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approach of distributed smart cameras [1] can be adapted to localize to solving this localization problem by equipping each of the modular robotic components and, hence, to facilitate these modules in the ensemble ...
This scheme was later revisited by Rekleitis et al [5] , and a planar version implemented using range and azimuth information obtained from a camera system. ...
Once the left leg and torso are docked, the torso module changes its blinker pattern. This serves as a signal for the other leg cluster to begin its approach and docking sequence. ...
doi:10.1109/icdsc.2007.4357508
dblp:conf/icdsc/ShirmohammadiYSPT07
fatcat:r4o5brzzyjhyfhgzjmfufy3fca
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