Dmitri Beglov, PhD
Research Assistant Professor
Boston University College of Engineering
Biomedical Engineering

PhD, Moscow Physics and Technical Institute



Dr. Dmitri Beglov was trained in molecular biophysics and computational chemistry. He is currently working on development of methods for realistic computer simulations of macromolecules. Such simulations help to predict and understand protein structure and interactions of proteins with each other, with organic molecules and solvent. His current interest is in development of effective algorithms and forcefield potentials to account for protein flexibility in computational docking.


Development of Structure Based Potential for Protein Mapping
09/20/2017 - 09/19/2018 (Subcontract PI)
Acpharis, Inc. NIH NIGMS
1R41GM123870-01A1



Title


Yr Title Project-Sub Proj Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

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  1. Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J Chem Inf Model. 2024 Mar 25; 64(6):2084-2100.View Related Profiles. PMID: 38456842
     
  2. Chen N, Yu D, Beglov D, Kon M, Castrillon-Candas JE. Uncertainty quantification of receptor ligand binding sites prediction. ArXiv. 2024 Jan 23. PMID: 38344224; PMCID: PMC10854274
     
  3. Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins. 2023 Dec; 91(12):1658-1683.View Related Profiles. PMID: 37905971; PMCID: PMC10841881; DOI: 10.1002/prot.26609;
     
  4. Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Beglov D, Vajda S, Kozakov D. The ClusPro AbEMap web server for the prediction of antibody epitopes. Nat Protoc. 2023 Jun; 18(6):1814-1840.View Related Profiles. PMID: 37188806; PMCID: PMC10898366; DOI: 10.1038/s41596-023-00826-7;
     
  5. Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc. 2023 Apr 05; 145(13):7123-7135.View Related Profiles. PMID: 36961978; PMCID: PMC10240388; DOI: 10.1021/jacs.2c09387;
     
  6. Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc. 2023 Apr 05; 145(13):7123-7135.View Related Profiles. PMID: 36961978; PMCID: PMC10240388; DOI: 10.1021/jacs.2c09387;
     
  7. Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Sabitova M, Beglov D, Vajda S, Kozakov D. Mapping of antibody epitopes based on docking and homology modeling. Proteins. 2023 Feb; 91(2):171-182.View Related Profiles. PMID: 36088633; PMCID: PMC9822860; DOI: 10.1002/prot.26420;
     
  8. Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, Keseru GM, Whitty A, Vajda S. Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J Chem Inf Model. 2020 12 28; 60(12):6612-6623.View Related Profiles. PMID: 33291870; PMCID: PMC8200320; DOI: 10.1021/acs.jcim.0c00877;
     
  9. Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Schueler-Furman O, Vajda S, Kozakov D. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. Proteins. 2020 08; 88(8):1082-1090.View Related Profiles. PMID: 32142178; PMCID: PMC7874234; DOI: 10.1002/prot.25887;
     
  10. Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. Structure-Based Analysis of Cryptic-Site Opening. Structure. 2020 02 04; 28(2):223-235.e2.View Related Profiles. PMID: 31810712; PMCID: PMC7004864; DOI: 10.1016/j.str.2019.11.007;
     
Showing 10 of 55 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 54 publications over 17 distinct years, with a maximum of 8 publications in 2014

YearPublications
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20072
20094
20102
20112
20125
20136
20148
20152
20162
20174
20182
20195
20202
20221
20233
20242

Contact for Mentoring:

44 Cummington St, Boston MA 02215
Boston MA 02215
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617.353.7123
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