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Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space.
Particle swarm optimization, proceedings of ieee international conference on neural networks (icnn’95) in
Kennedy, J. and Eberhart, R. (1995) · 1995
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Adaptive simulated annealing (ASA): lessons learned
Ingber, L. (2000) · 2000
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The particle swarm-explosion, stability, and convergence in a multidimensional complex space
Clerc, M. and Kennedy, J. (2002) · 2002
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A Distribution-Free Theory of Nonparametric Regression
Györfi, L · 2002
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Prediction of protein–protein interactions by docking methods
Smith, G. R. and Sternberg, M. J. (2002) · 2002
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Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
Gray, J. J · 2003
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Optimal clustering for detecting near-native conformations in protein docking
Kozakov, D · 2005
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Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
Méndez, R · 2005
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An informational approach to the global optimization of expensive-to-evaluate functions
Villemonteix, J · 2006
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Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking
Shen, Y · 2007
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Protein docking by the underestimation of free energy funnels in the space of encounter complexes
Shen, Y · 2008
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CHARMM: the biomolecular simulation program
Brooks, B. R · 2009
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Aleatoric or epistemic? does it matter?
Der Kiureghian, A. and Ditlevsen, O. (2009) · 2009
Cited alongside, same era.
Convergence and combination of methods in protein–protein docking
Vajda, S. and Kozakov, D. (2009) · 2009
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Protein-Protein Docking Benchmark Version 4.0
Hwang, H · 2010
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Are Scoring Functions in Protein-Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
Kastritis, P. L. and Bonvin, A. M. J. J. (2010) · 2010
Cited alongside, same era.
SwarmDock and the Use of Normal Modes in Protein-Protein Docking
Moal, I. H. and Bates, P. A. (2010) · 2010
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Analysis of Thompson Sampling for the multi-armed bandit problem
Protein–protein binding affinity prediction from amino acid sequence
Yugandhar, K. and Gromiha, M. M. (2014) · 2014
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Energy minimization on manifolds for docking flexible molecules
Mirzaei, H · 2015
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cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions
Oliwa, T. and Shen, Y. (2015) · 2015
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Estimation of Uncertainties in the Global Distance Test (GDT_ts) for CASP Models
Li, W · 2016
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Taking the Human Out of the Loop: A Review of Bayesian Optimization
Shahriari, B · 2016
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Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility
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Agrawal, S. and Goyal, N. (2011) · 2011
Cited alongside, same era.
An Empirical Evaluation of Thompson Sampling
Chapelle, O. and Li, L. (2011) · 2011
Cited alongside, same era.
Geostatistics: Modeling Spatial Uncertainty, 2nd Edition
Chilès, J.-P. and Delfiner, P. (2012) · 2012
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A Nonparametric Conjugate Prior Distribution for the Maximizing Argument of a Noisy Function
Ortega, P · 2012
Cited alongside, same era.
Interactome3d: adding structural details to protein networks
Mosca, R · 2013
Cited alongside, same era.
Improved flexible refinement of protein docking in capri rounds 22–27
Shen, Y. (2013) · 2013
Cited alongside, same era.
Predictive Entropy Search for Efficient Global Optimization of Black-box Functions
Henrández-Lobato, J. M · 2014
Cited alongside, same era.
Chen, H · 2017
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Lightdock: a new multi-scale approach to protein–protein docking
Jiménez-García, B · 2017
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Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling
Rasheed, M · 2017
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A Tutorial on Thompson Sampling
Russo, D · 2017
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Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets
Marze, N. A · 2018
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Refinement of protein-protein complexes in contact map space with metadynamics simulations
Pfeiffenberger, E. and Bates, P. A. (2018) · 2018
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