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Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

Frontiers in molecular biosciences, 2019-10, Vol.6, p.112-112

2019

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Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

Journal of computer-aided molecular design, 2020-02, Vol.34 (2), p.179-189

2020

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Generalization Second Order Macroscopic Traffic Models via Relative Velocity of the Congestion Propagation

Mathematics (Basel), 2021-08, Vol.9 (16), p.2001

2021

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Protein-Protein and Protein-Peptide Docking with ClusPro Server

Methods in molecular biology (Clifton, N.J.), 2020-01, Vol.2165, p.157

2020

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ClusPro LigTBM: Automated Template-based Small Molecule Docking

Journal of molecular biology, 2020-05, Vol.432 (11), p.3404-3410

2020

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Traffic flow speed prediction on transportation graph with convolutional neural networks

Kompʹûternye issledovaniâ i modelirovanie (Online), 2018-06, Vol.10 (3), p.359-367

2018

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Enhanced Sampling of Peptide Binding to Proteins through Gaussian Accelerated Molecular Dynamics Simulations

Biophysical journal, 2020-02, Vol.118 (3), p.139a-139a

2020

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The Norway spruce genome sequence and conifer genome evolution

Nature (London), 2013, Vol.497 (7451), p.579-584

2013

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Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Journal of medicinal chemistry, 2019-07, Vol.62 (14), p.6512-6524

2019

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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins, structure, function, and bioinformatics, 2021-12, Vol.89 (12), p.1800-1823

2021

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Bayesian localization for autonomous vehicle using sensor fusion and traffic signs

Kompʹûternye issledovaniâ i modelirovanie (Online), 2018-06, Vol.10 (3), p.295-303

2018

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Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

Proteins, structure, function, and bioinformatics, 2019-12, Vol.87 (12), p.1241-1248

2019

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SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies

Journal of computational chemistry, 2016-06, Vol.37 (17), p.1537-1551

2016

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Development, calibration and verification of mathematical model for multilane urban road traffic flow. Part II

Kompʹûternye issledovaniâ i modelirovanie (Online), 2015-12, Vol.7 (6), p.1205-1219

2015

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Developing the mathematical model of road junction by the hydrodynamic approach

Kompʹûternye issledovaniâ i modelirovanie (Online), 2014-08, Vol.6 (4), p.503-522

2014

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ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking

Proteins, structure, function, and bioinformatics, 2020-08, Vol.88 (8), p.1082-1090

2020

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Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

Journal of computer-aided molecular design, 2019-01, Vol.33 (1), p.119-127

2019

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Development, calibration and verification of mathematical model for multilane urban road traffic flow. Part I

Kompʹûternye issledovaniâ i modelirovanie (Online), 2015-12, Vol.7 (6), p.1185-1203

2015

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Protein–ligand docking using FFT based sampling: D3R case study

Journal of computer-aided molecular design, 2018-01, Vol.32 (1), p.225-230

2018

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CUDA and OpenCL implementations of Conways Game of Life cellular automata

Kompʹûternye issledovaniâ i modelirovanie (Online), 2010-09, Vol.2 (3), p.323-326

2010

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Molecular Mechanisms, Thermodynamics, and Dissociation Kinetics of Knob-Hole Interactions in Fibrin

The Journal of biological chemistry, 2013-08, Vol.288 (31), p.22681-22692

2013

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Phase transition from -helices to -sheets in supercoils of fibrillar proteins

Kompʹûternye issledovaniâ i modelirovanie (Online), 2013-08, Vol.5 (4), p.705-725

2013

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Ensemble building and statistical mechanics methods for MHC-peptide binding prediction

Kompʹûternye issledovaniâ i modelirovanie (Online), 2020-12, Vol.12 (6), p.1383-1395

2020

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Bayesian Framework for Vehicle Localization Using Crowdsourced Data

2018 IEEE Intelligent Vehicles Symposium (IV), 2018, p.215-219

2018

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Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

Generalization Second Order Macroscopic Traffic Models via Relative Velocity of the Congestion Propagation

Protein-Protein and Protein-Peptide Docking with ClusPro Server

ClusPro LigTBM: Automated Template-based Small Molecule Docking

Traffic flow speed prediction on transportation graph with convolutional neural networks

Enhanced Sampling of Peptide Binding to Proteins through Gaussian Accelerated Molecular Dynamics Simulations

The Norway spruce genome sequence and conifer genome evolution

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Bayesian localization for autonomous vehicle using sensor fusion and traffic signs

Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies

Development, calibration and verification of mathematical model for multilane urban road traffic flow. Part II

Developing the mathematical model of road junction by the hydrodynamic approach

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

Development, calibration and verification of mathematical model for multilane urban road traffic flow. Part I

Protein–ligand docking using FFT based sampling: D3R case study

CUDA and OpenCL implementations of Conways Game of Life cellular automata

Molecular Mechanisms, Thermodynamics, and Dissociation Kinetics of Knob-Hole Interactions in Fibrin

Phase transition from -helices to -sheets in supercoils of fibrillar proteins

Ensemble building and statistical mechanics methods for MHC-peptide binding prediction

Bayesian Framework for Vehicle Localization Using Crowdsourced Data

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells

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