Dmitri Beglov

发表

ClusPro: Performance in CAPRI rounds 6–11 and the new server

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2007, Proteins.

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

Andrey Alekseenko, Dima Kozakov, Dmitri Beglov, 2019, Proteins.

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2015, Nature Protocols.

The ClusPro web server for protein–protein docking

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Nature Protocols.

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

Mohammad Moghadasi, Dima Kozakov, Dmitri Beglov, 2017, Journal of Computer-Aided Molecular Design.

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, J. Comput. Aided Mol. Des..

How good is automated protein docking?

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Proteins.

Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2010, Proteins.

Author response for "ClusPro in rounds 38‐45 of CAPRI: Toward combining template‐based methods with free docking"

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2019 .

Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2007, Proteins.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

A new approach to rigid body minimization with application to molecular docking

Ioannis Ch. Paschalidis, Dima Kozakov, Dmitri Beglov, 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT

Dima Kozakov, Dmitri Beglov, Ora Schueler-Furman, 2017, Bioinform..

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, Bioinform..

New additions to the ClusPro server motivated by CAPRI

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Proteins.

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

Andrey Alekseenko, Dima Kozakov, Dmitri Beglov, 2020, Proteins.

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Bioinform..

FTMAP: extended protein mapping with user-selected probe molecules

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2012, Nucleic Acids Res..

Docking Server for the Identification of Heparin Binding Sites on Proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, J. Chem. Inf. Model..

Application of asymmetric statistical potentials to antibody-protein docking

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Bioinform..

Flexible refinement of protein-ligand docking on manifolds

Ioannis Ch. Paschalidis, Dima Kozakov, Dmitri Beglov, 2013, 52nd IEEE Conference on Decision and Control.

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2014, Journal of chemical theory and computation.

Encounter complexes and dimensionality reduction in protein–protein association

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, eLife.

Where does amantadine bind to the influenza virus M2 proton channel?

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2010, Trends in biochemical sciences.

Energy Minimization on Manifolds for Docking Flexible Molecules.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2015, Journal of chemical theory and computation.

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2012, Journal of chemical theory and computation.

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Nucleic acids research.

The structural basis of pregnane X receptor binding promiscuity.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2009, Biochemistry.

How Proteins Bind Macrocycles

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, Nature chemical biology.

Detection of peptide‐binding sites on protein surfaces: The first step toward the modeling and targeting of peptide‐mediated interactions

Dima Kozakov, Dmitri Beglov, Tanggis Bohnuud, 2013, Proteins.

Exploring the structural origins of cryptic sites on proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2018, Proceedings of the National Academy of Sciences.

Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel.

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, Biophysical journal.

Minimal ensembles of side chain conformers for modeling protein–protein interactions

Roland L Dunbrack, Roland L. Dunbrack, Dima Kozakov, 2012, Proteins.