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

by Jinan Wang, Andrey Alekseenko, Andrey Alekseenko, Dima Kozakov, Dima Kozakov, Yinglong Miao
Published 2019-10-01

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

by Tanggis Bohnuud, Dima Kozakov, Sandor Vajda
Published 2014-10-01

Improved prediction of MHC-peptide binding using protein language models

by Nasser Hashemi, Boran Hao, Mikhail Ignatov, Mikhail Ignatov, Ioannis Ch. Paschalidis, Ioannis Ch. Paschalidis, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Sandor Vajda, Sandor Vajda, Dima Kozakov, Dima Kozakov, Dima Kozakov
Published 2023-08-01

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

by Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A Porter, Dima Kozakov, Ora Schueler-Furman
Published 2017-12-01

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

by Shahabeddin Sotudian, Israel T. Desta, Nasser Hashemi, Shahrooz Zarbafian, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
Published 2021-01-01

Conservation of binding properties in protein models

by Megan Egbert, Kathryn A. Porter, Usman Ghani, Sergei Kotelnikov, Thu Nguyen, Ryota Ashizawa, Dima Kozakov, Sandor Vajda
Published 2021-01-01

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

by Pierre C. Havugimana, Raghuveera Kumar Goel, Sadhna Phanse, Ahmed Youssef, Dzmitry Padhorny, Sergei Kotelnikov, Dima Kozakov, Andrew Emili
Published 2022-07-01

Encounter complexes and dimensionality reduction in protein–protein association

by Dima Kozakov, Keyong Li, David R Hall, Dmitri Beglov, Jiefu Zheng, Pirooz Vakili, Ora Schueler-Furman, Ioannis Ch Paschalidis, G Marius Clore, Sandor Vajda
Published 2014-04-01

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

by Shawn Hingtgen, Randa Kasmieh, Elizabeth Elbayly, Irina Nesterenko, Jose-Luiz Figueiredo, Rupesh Dash, Devanand Sarkar, David Hall, Dima Kozakov, Sandor Vajda, Paul B Fisher, Khalid Shah
Published 2012-01-01

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

by Indranil Paul, Dante Bolzan, Ahmed Youssef, Keith A. Gagnon, Heather Hook, Gopal Karemore, Michael U. J. Oliphant, Weiwei Lin, Qian Liu, Sadhna Phanse, Carl White, Dzmitry Padhorny, Sergei Kotelnikov, Christopher S. Chen, Pingzhao Hu, Gerald V. Denis, Dima Kozakov, Brian Raught, Trevor Siggers, Stefan Wuchty, Senthil K. Muthuswamy, Andrew Emili
Published 2023-02-01

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

by Weiwei Lin, Weiwei Lin, Fatemeh Mousavi, Benjamin C. Blum, Benjamin C. Blum, Christian F. Heckendorf, Christian F. Heckendorf, Jarrod Moore, Jarrod Moore, Noah Lampl, Noah Lampl, Mark McComb, Mark McComb, Sergei Kotelnikov, Wenqing Yin, Nabil Rabhi, Matthew D. Layne, Dima Kozakov, Vipul C. Chitalia, Vipul C. Chitalia, Vipul C. Chitalia, Andrew Emili, Andrew Emili, Andrew Emili
Published 2023-11-01

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

by Weiwei Lin, Weiwei Lin, Fatemeh Mousavi, Benjamin C. Blum, Benjamin C. Blum, Christian F Heckendorf, Christian F Heckendorf, Jarrod Moore, Jarrod Moore, Noah Lampl, Noah Lampl, Mark McComb, Mark McComb, Sergei Kotelnikov, Wenqing Yin, Nabil Rabhi, Matthew D. Layne, Dima Kozakov, Vipul C. Chitalia, Vipul C. Chitalia, Vipul C. Chitalia, Andrew Emili, Andrew Emili, Andrew Emili
Published 2024-02-01

Docking Server for the Identification of Heparin Binding Sites on Proteins

by Mottarella, Scott E., Beglov, Dmitri, Beglova, Natalia, Nugent, Matthew A., Kozakov, Dima, Vajda, Sandor
Published 2015

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

by Hingtgen, Shawn, Kasmieh, Randa, Elbayly, Elizabeth, Nesterenko, Irina, Figueiredo, Jose-Luiz, Dash, Rupesh, Sarkar, Devanand, Hall, David, Kozakov, Dima, Vajda, Sandor, Fisher, Paul B., Shah, Khalid A.
Published 2013

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

by Luo, Lingqi, Kozakov, Dima, Vajda, Sandor, Allen, Karen N., Lukose, Vinita, Imperiali, Barbara
Published 2017