List of works - Dima Kozakov

A New Approach to Rigid Body Minimization with Application to Molecular Docking

scientific article published on December 2012

A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking(*)

scientific article

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking

scientific article

A benchmark testing ground for integrating homology modeling and protein docking

scientific article

A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy

scientific article

A message passing approach to Side Chain Positioning with applications in protein docking refinement

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

scientific article published on 14 December 2020

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

scientific article published on 30 June 2008

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro

scientific article published on 10 June 2015

Accounting for pairwise distance restraints in FFT-based protein-protein docking.

scientific article published on 29 June 2016

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

scientific article

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

scientific article published on 01 January 2021

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

scientific article

Analysis of protein binding sites by computational solvent mapping

scientific article

Application of asymmetric statistical potentials to antibody-protein docking

scientific article

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery

scientific article published on 08 December 2020

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

scientific article

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

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication.

scientific article

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

scientific article published on 06 March 2020

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking

scientific article published on 19 October 2016

ClusPro: performance in CAPRI rounds 6-11 and the new server

scientific article published in December 2007

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface

scientific article published on 10 April 2013

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

scientific article

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

scientific article published on 24 November 2015

Convergence and combination of methods in protein-protein docking

scientific article published on 25 March 2009

DARS (Decoys As the Reference State) potentials for protein-protein docking

scientific article published on August 2008

Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

scientific article

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

scientific article

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

scientific article published on 17 October 2013

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

scientific article

Docking server for the identification of heparin binding sites on proteins

scientific article

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

scientific article published on December 2007

Domain motion and interdomain hot spots in a multidomain enzyme

scientific article published on September 2010

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations

scientific article

Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional Fourier transform

Encounter complexes and dimensionality reduction in protein-protein association

scientific article published on 08 April 2014

Energy Minimization on Manifolds for Docking Flexible Molecules

scientific article published on 13 February 2015

Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces

scientific article (publication date: October 2014)

Evolutionary origins of the estrogen signaling system: insights from amphioxus

scientific article

FTMAP: extended protein mapping with user-selected probe molecules

scientific article

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

scientific article published on 22 November 2011

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

scientific article published on 21 December 2016

Flexible Refinement of Protein-Ligand Docking on Manifolds

scientific article published on January 2013

Focused grid-based resampling for protein docking and mapping

scientific article published on 2 February 2016

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

scientific article

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

scientific article published on 15 December 2011

How good is automated protein docking?

scientific article published on 17 October 2013

How proteins bind macrocycles.

scientific article

Insights into the architecture of the eIF2Bα/β/δ regulatory subcomplex

scientific article

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

scientific article published on 02 January 2020

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

scientific article published on 05 July 2019

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

scientific article

Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro

scientific article

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

scientific article

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

scientific article published on 31 December 2019

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

scientific article published on 12 November 2018

New Frontiers in Druggability

scientific article published on 31 July 2015

New additions to the ClusPro server motivated by CAPRI.

scientific article published on 9 December 2016

Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles

scientific article published on 04 October 2023

Optimal clustering for detecting near-native conformations in protein docking

scientific article

Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach

scientific article published on December 2014

Organization of the human mitochondrial transcription initiation complex

scientific article published on 09 January 2014

PIPER: an FFT-based protein docking program with pairwise potentials

scientific article published in November 2006

Predicting Protein Dimer Structures Using MELD × MD

scientific article published on 05 April 2019

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

scientific article

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

scientific article published on 3 November 2017

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

scientific article published on 13 July 2016

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces

scientific article published on 24 July 2012

Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F

scientific article

Rigid Body Energy Minimization on Manifolds for Molecular Docking

scientific article published on 21 August 2012

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

scientific article

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

scientific article published on 26 December 2019

Sampling and scoring: a marriage made in heaven

scientific article

Stimulators of translation identified during a small molecule screening campaign

scientific article

Structural conservation of druggable hot spots in protein-protein interfaces

scientific article

Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.

scientific article published on December 2009

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

scientific article published on 01 October 2019

The ClusPro web server for protein-protein docking

scientific article published on 12 January 2017

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

scientific article published on 9 April 2015

The impact of side-chain packing on protein docking refinement

scientific article

The structural basis of pregnane X receptor binding promiscuity

scientific article published on December 2009

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

scientific article

List of works by Dima Kozakov

A New Approach to Rigid Body Minimization with Application to Molecular Docking

A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking(*)

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking

A benchmark testing ground for integrating homology modeling and protein docking

A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy

A message passing approach to Side Chain Positioning with applications in protein docking refinement

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro

Accounting for pairwise distance restraints in FFT-based protein-protein docking.

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

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

Analysis of protein binding sites by computational solvent mapping

Application of asymmetric statistical potentials to antibody-protein docking

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery

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

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

Blind prediction of interfacial water positions in CAPRI

Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication.

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

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking

ClusPro: performance in CAPRI rounds 6-11 and the new server

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface

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

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

Convergence and combination of methods in protein-protein docking

DARS (Decoys As the Reference State) potentials for protein-protein docking

Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server

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

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

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

Docking server for the identification of heparin binding sites on proteins

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

Domain motion and interdomain hot spots in a multidomain enzyme

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations

Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional Fourier transform

Encounter complexes and dimensionality reduction in protein-protein association

Energy Minimization on Manifolds for Docking Flexible Molecules

Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces

Evolutionary origins of the estrogen signaling system: insights from amphioxus

FTMAP: extended protein mapping with user-selected probe molecules

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

Flexible Refinement of Protein-Ligand Docking on Manifolds

Focused grid-based resampling for protein docking and mapping

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

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

How good is automated protein docking?

How proteins bind macrocycles.

Insights into the architecture of the eIF2Bα/β/δ regulatory subcomplex

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro

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

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

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

New Frontiers in Druggability

New additions to the ClusPro server motivated by CAPRI.

Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles

Optimal clustering for detecting near-native conformations in protein docking

Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach

Organization of the human mitochondrial transcription initiation complex

PIPER: an FFT-based protein docking program with pairwise potentials

Predicting Protein Dimer Structures Using MELD × MD

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

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

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces

Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F

Rigid Body Energy Minimization on Manifolds for Molecular Docking

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

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

Sampling and scoring: a marriage made in heaven

Stimulators of translation identified during a small molecule screening campaign

Structural conservation of druggable hot spots in protein-protein interfaces

Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.