D. Kozakov

发表

Structural conservation of druggable hot spots in protein–protein interfaces

Laurie E. Grove, S. Vajda, D. Kozakov, 2011, Proceedings of the National Academy of Sciences.

PIPER: An FFT‐based protein docking program with pairwise potentials

Stephen R. Comeau, S. Vajda, D. Kozakov, 2006, Proteins.

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

Dima Kozakov, Sandor Vajda, Dzmitry Padhorny, 2017, Journal of molecular biology.

Optimal clustering for detecting near-native conformations in protein docking.

Dima Kozakov, Sandor Vajda, Karl H. Clodfelter, 2005, Biophysical journal.

Insights into the Architecture of the eIF2Bα/β/δ Regulatory Subcomplex

S. Vajda, D. Kozakov, B. Xia, 2014, Biochemistry.

Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication

S. Vajda, R. Dingledine, D. Kozakov, 2011, Journal of Virology.

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.

Kathryn A. Porter, S. Vajda, J. Wells, 2019, Journal of medicinal chemistry.

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

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

Domain motion and interdomain hot spots in a multidomain enzyme

Brandon S. Zerbe, S. Vajda, D. Kozakov, 2010, Protein science : a publication of the Protein Society.

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

B. Blencowe, A. Emili, S. Wuchty, 2020, Molecular Cell.

Encounter complexes and dimensionality reduction in protein–protein association

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

Ligand Binding and Activation of PPARγ by Firemaster® 550: Effects on Adipogenesis and Osteogenesis in Vitro

S. Vajda, D. Kozakov, D. Beglov, 2014, Environmental health perspectives.

How Proteins Bind Macrocycles

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

Blind prediction of interfacial water positions in CAPRI

Kengo Kinoshita, Haruki Nakamura, Xiaoqin Zou, 2014, Proteins.

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Trends in pharmacological sciences.

New Frontiers in Druggability.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Journal of medicinal chemistry.

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

Elizabeth A. Villar, Brandon S. Zerbe, Marianna K. Sayeg, 2013, Journal of the American Chemical Society.

Structural insights into recognition of β2‐glycoprotein I by the lipoprotein receptors

S. Vajda, D. Kozakov, Ryan Brenke, 2009, Proteins.

Analysis of protein binding sites by computational solvent mapping.

Dima Kozakov, Sandor Vajda, David R Hall, 2012, Methods in molecular biology.

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

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

FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.

S. Vajda, D. Kozakov, M. Egbert, 2022, Journal of molecular biology.

Exploring the structural origins of cryptic sites on proteins

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

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

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, bioRxiv.

AXS : Ultra-fast mall-Angle X-ray in Protein Docking and

D. Kozakov, Andrey M. Kazennov, Mikhail Ignatov, 2018 .

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

O. Schueler‐Furman, D. Kozakov, George Jones, 2017, Methods in molecular biology.

A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy

S. Vajda, P. Fisher, K. Shah, 2012, PloS one.

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

O. Schueler‐Furman, K. Dill, S. Vajda, 2019, Proteins.

Evolutionary origins of the estrogen signaling system: Insights from amphioxus

S. Vajda, D. Kozakov, A. Tarrant, 2011, The Journal of Steroid Biochemistry and Molecular Biology.

The N34S mutation of SPINK1 may impact the kinetics of trypsinogen activation to cause early trypsin release in the pancreas

S. Vajda, D. Kozakov, Zhuyezi Sun, 2020, bioRxiv.

API Development Increases Access to Shared Computing Resources at Boston University

Amanda E. Wakefield, S. Vajda, D. Kozakov, 2022, Journal of Software Engineering and Applications.

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

Amanda E. Wakefield, S. Vajda, G. Keserü, 2020, J. Chem. Inf. Model..

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking

Dima Kozakov, Sandor Vajda, Taner Kaya, 2008, BIOCOMP.

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

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

Mapping the binding sites of challenging drug targets.

Amanda E. Wakefield, S. Vajda, D. Kozakov, 2022, Current opinion in structural biology.

Docking Server for the Identification of Heparin Binding Sites on Proteins

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

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

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

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

Brandon S. Zerbe, S. Vajda, D. Kozakov, 2013 .

Analysis of binding site hot spots on the surface of Ras GTPase.

Dima Kozakov, Sandor Vajda, Carla Mattos, 2011, Journal of molecular biology.

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

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

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

A. Emili, S. Phanse, P. Havugimana, 2022, Nature Communications.

Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro

S. Vajda, D. Kozakov, D. Padhorny, 2021, bioRxiv.

Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme

Dima Kozakov, Sandor Vajda, Christine Yueh, 2011, Journal of the American Chemical Society.

Computational Methods to Support Fragment‐based Drug Discovery

Dima Kozakov, Sandor Vajda, Laurie E. Grove, 2016 .

Performance and Its Limits in Rigid Body Protein-Protein Docking.

Kathryn A. Porter, S. Vajda, D. Kozakov, 2020, Structure.

Conservation and Covariance in Monotopic Phosphoglycosyltransferases Identifies the Functional Catalytic Core

Karen N. Allen, S. Vajda, B. Imperiali, 2015 .

Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors

Amanda E. Wakefield, S. Vajda, G. Keserü, 2022, J. Chem. Inf. Model..

Organization of the human mitochondrial transcription initiation complex

D. Kozakov, D. Beglov, M. García-Díaz, 2014, Nucleic acids research.

Stimulators of translation identified during a small molecule screening campaign.

S. Vajda, D. Kozakov, D. Hall, 2014, Analytical biochemistry.

Mapping of antibody epitopes based on docking and homology modeling

S. Vajda, D. Kozakov, D. Beglov, 2022, Proteins.

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

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

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).

Karen N. Allen, Amanda E. Wakefield, S. Vajda, 2019, Biochemistry.

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

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, Bioinform..

The ClusPro web server for protein–protein docking

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

How good is automated protein docking?

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

A critical overview of computational approaches employed for COVID-19 drug discovery

Tudor I. Oprea, Rommie E. Amaro, G. Schneider, 2021, Chemical Society reviews.

A benchmark testing ground for integrating homology modeling and protein docking

Zhiping Weng, Alexandre M J J Bonvin, Dima Kozakov, 2017, Proteins.

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

Karen N. Allen, S. Vajda, B. Imperiali, 2015, Biochemistry.

ClusPro LigTBM: Automated Template-Based Small Molecule Docking.

Andrey Alekseenko, Dima Kozakov, Sandor Vajda, 2019, Journal of molecular biology.

What method to use for protein-protein docking?

Dima Kozakov, Sandor Vajda, Kathryn A Porter, 2019, Current opinion in structural biology.

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

Bing Xia, Dima Kozakov, Ora Schueler-Furman, 2017, bioRxiv.

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

Dima Kozakov, Sandor Vajda, Yaroslav Kholodov, 2016, Proceedings of the National Academy of Sciences.

AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence

D. Kozakov, D. Standley, Songling Li, 2022, Bioinformatics advances.

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

S. Vajda, R. Dingledine, D. Kozakov, 2010, Proceedings of the National Academy of Sciences.

Allostery in Its Many Disguises: From Theory to Applications.

Ruth Nussinov, Ivet Bahar, Dima Kozakov, 2019, Structure.

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.

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

A. Emili, G. Karemore, S. Wuchty, 2021, bioRxiv.

New additions to the ClusPro server motivated by CAPRI

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

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

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2008, Biophysical journal.

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.

Application of asymmetric statistical potentials to antibody-protein docking

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

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

Jeffrey J. Gray, Panagiotis I. Koukos, Johnathan D. Guest, 2021, Proteins.

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

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

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..

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

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

Side-chain Packing Using SE(3)-Transformer

S. Vajda, D. Kozakov, R. Chowdhury, 2021, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Improved cluster ranking in protein–protein docking using a regression approach

P. Vakili, I. Paschalidis, S. Vajda, 2021, Computational and structural biotechnology journal.

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.

Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes

I. Paschalidis, S. Vajda, D. Kozakov, 2018, Scientific Reports.

Focused grid‐based resampling for protein docking and mapping

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2016, J. Comput. Chem..

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

David W. Ritchie, Dima Kozakov, Sandor Vajda, 2008, Bioinform..

Protein folds vs. protein folding: Differing questions, different challenges

Julie C. Mitchell, R. Nussinov, J. Skolnick, 2022, Proceedings of the National Academy of Sciences of the United States of America.

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

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

Improved Predictions of MHC-Peptide Binding using Protein Language Models

P. Vakili, I. Paschalidis, S. Vajda, 2022, bioRxiv.

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

Dima Kozakov, Marc F. Lensink, Nawsad Alam, 2017, Proteins.

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

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

The Impact of Side-Chain Packing on Protein Docking Refinement

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2015, J. Chem. Inf. Model..

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

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2014, 53rd IEEE Conference on Decision and Control.

A new distributed algorithm for side-chain positioning in the process of protein docking

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

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

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

Ligand deconstruction: Why some fragment binding positions are conserved and others are not

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Proceedings of the National Academy of Sciences.

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

Andrey Alekseenko, Dima Kozakov, Ken A. Dill, 2019, Journal of Computer-Aided Molecular Design.

Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap

S. Vajda, D. Kozakov, D. Padhorny, 2022, Acta crystallographica. Section D, Structural biology.

Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1.

C. Abbas, D. Kozakov, D. Padhorny, 2018, The international journal of biochemistry & cell biology.

Progress toward improved understanding of antibody maturation.

Kathryn A. Porter, S. Vajda, D. Kozakov, 2021, Current opinion in structural biology.

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

Bing Xia, Dima Kozakov, Sandor Vajda, 2016, Bioinform..

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.

The structural basis of pregnane X receptor binding promiscuity.

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

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT

A. Emili, G. Karemore, S. Wuchty, 2023, Nature Communications.

Protein-Protein and Protein-Peptide Docking with ClusPro Server.

Andrey Alekseenko, Dima Kozakov, Mikhail Ignatov, 2020, Methods in molecular 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.

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

46 Encounter complexes and dimensionality reduction in protein-protein association

Dima Kozakov, Sandor Vajda, Pirooz Vakili, 2015, Journal of biomolecular structure & dynamics.

Convergence and combination of methods in protein-protein docking.

Dima Kozakov, Sandor Vajda, S. Vajda, 2009, Current opinion in structural biology.

Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro

Bing Xia, Ioannis Ch. Paschalidis, Dima Kozakov, 2015, J. Comput. Chem..

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

Cong Liu, Dima Kozakov, Yaroslav Kholodov, 2018, Journal of Computer-Aided Molecular Design.

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

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

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, Frontiers in molecular biosciences.

FTMAP: extended protein mapping with user-selected probe molecules

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

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Dima Kozakov, Sandor Vajda, Tanggis Bohnuud, 2014, PLoS Comput. Biol..

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

D. Kozakov, Y. Kholodov, Andrey Alekseenko, 2020 .

180 Towards the high-resolution, ab initio modeling of peptide-mediated interactions

O. Schueler‐Furman, D. Kozakov, N. London, 2015, Journal of biomolecular structure & dynamics.

Conservation of binding properties in protein models

Kathryn A. Porter, S. Vajda, D. Kozakov, 2021, Computational and structural biotechnology journal.

High Accuracy Prediction of PROTAC Complex Structures.

S. Vajda, G. Poda, D. Kozakov, 2023, Journal of the American Chemical Society.

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

L. C. Andrews, H. Bernstein, D. Kozakov, 2020, bioRxiv.

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

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

Predicting Protein Dimer Structures Using MELD × MD.

K. Dill, D. Kozakov, Emiliano Brini, 2019, Journal of chemical theory and computation.

Energy Minimization on Manifolds for Docking Flexible Molecules.

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

Flexible refinement of protein-ligand docking on manifolds

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

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

S. Vajda, B. Imperiali, D. Kozakov, 2015, Biochemistry.

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

Stephen R. Comeau, S. Vajda, D. Kozakov, 2008, Biophysical journal.

Convergence and combination of methods in protein-protein docking.

S. Vajda, D. Kozakov, 2009, Current opinion in structural biology.

Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication

S. Vajda, R. Dingledine, D. Kozakov, 2011, Journal of Virology.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Johnathan D. Guest, Adam K. Sieradzan, Charles W Christoffer, 2023, Proteins.

The ClusPro AbEMap web server for the prediction of antibody epitopes

S. Vajda, D. Kozakov, D. Beglov, 2023, Nature Protocols.

Integrated metabolomics and proteomics reveal biomarkers associated with hemodialysis in end-stage kidney disease

D. Kozakov, B. Blum, V. Chitalia, 2023, Frontiers in pharmacology.

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

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

Blind prediction of interfacial water positions in CAPRI

Julie C. Mitchell, Jeffrey J. Gray, H. Wolfson, 2014, Proteins.

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

Dima Kozakov, Sandor Vajda, Ora Schueler-Furman, 2008, Proteins.

The ClusPro web server for protein–protein docking

Kathryn A. Porter, S. Vajda, D. Kozakov, 2017, Nature Protocols.

Assessing the binding properties of CASP14 targets and models

S. Vajda, D. Kozakov, D. Padhorny, 2021, Proteins.

ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking.

Dima Kozakov, Mikhail Ignatov, Andrey Kazennov, 2018, Journal of molecular biology.

Sampling and scoring: A marriage made in heaven

Dima Kozakov, Sandor Vajda, David R. Hall, 2013, Proteins.