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Ensemble docking revisited

Oliver Korb, S Bowden, T Olsson, D Frenkel, J Liebeschuetz, J Cole
2010 Journal of Cheminformatics  
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

Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone (+1 others)
2017 Journal of Computer-Aided Molecular Design  
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

William Sinko, Steffen Lindert, J. Andrew McCammon
2012 Chemical Biology and Drug Design  
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

Jesika Schilder, Wei-Min Liu, Pravin Kumar, Mark Overhand, Martina Huber, Marcellus Ubbink
2016 Physical Chemistry, Chemical Physics - PCCP  
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]

Michael L Drummond, Andrew Henry, Huifang Li, Christopher I Williams
2020 bioRxiv   pre-print
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

Horvath, Marcou, Varnek
2019 Molecules  
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

Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos
2006 Proteins: Structure, Function, and Bioinformatics  
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

Elodie Laine, Alessandra Carbone
2016 Proteins: Structure, Function, and Bioinformatics  
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

Chang Jun Lee, Vasu Chandrasekaran, Sangwook Wu, Robert E. Duke, Lee G. Pedersen
2010 Thrombosis Research  
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

Arvind Sivasubramanian, Aroop Sircar, Sidhartha Chaudhury, Jeffrey J. Gray
2009 Proteins: Structure, Function, and Bioinformatics  
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

Ilizaliturri-Flores Ian, Rosas-Trigueros Jorge Luis, Carrillo-Vazquez Jonathan Pablo, Vique-Sanchez Jose Luis, Carrillo-Ibarra Normande, Zamora-Lopez Beatriz, Reyes-Lopez Cesar Augusto Sandino, Benitez-Cardoza Claudia Guadalupe, Correa-Basurto Jose, Zamorano-Carrillo Absalom
2013 American Journal of Agricultural and Biological Science  
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

Sergey V. Solomatin, Max Greenfeld, Steven Chu, Daniel Herschlag
2010 Nature  
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]

Thuluz Meza Menchaca, Claudia Juárez-Portilla, Rossana C. Zepeda
2020 Drug Discovery and Development - New Advances [Working Title]  
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

Dmytro B. Kovalskyy, Dmitri N. Ivanov
2014 Biochemistry  
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

Babak Shirmohammadi, Camillo J. Taylor, Mark Yim, Jimmy Sastra, Mike Park
2007 2007 First ACM/IEEE International Conference on Distributed Smart Cameras  
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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