Research articles
Amination of a Green Solvent via Immobilized Biocatalysis for the Synthesis of Nemtabrutinib
CK Prier, KC Soto, JH Forstater, N Kuhl, JT Kuethe, WL Cheung-Lee, MJ Di Maso, CM Eberle, ST Grosser, H Ho, E Hoyt, A Maguire, KM Maloney, A Makarewicz, JP McMullen, JC Moore, GS Murphy, K Narsimhan, W Pan, NR Rivera, A Saha-Shah, DA Thaisrivongs, D Verma, A Wyatt, D Zewge
ACS Catalysis 2023, 13, 7707-7714 | https://doi.org/10.1021/acscatal.3c00941
Directed evolution to reverse epoxide hydrolase enantioselectivity for meso-3,4-epoxytetrahydrofuran
Kaori Hiraga, Tetsuji Itoh, Deeptak Verma, Wei Wang, Chen Huang, Michael Ardolino, Yong-Li Zhong, Grant Murphy
ChemCatChem (2023) e202300238 | https://doi.org/10.1002/cctc.202300238
Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening
Yongliang Fang, Andrew Y Chang, Deeptak Verma, Shin-Ichiro Miyashita, Susan Eszterhas, Pyung-Gang Lee, Yi Shen, Lydia R Davis, Min Dong, Chris Bailey-Kellogg, Karl E Griswold
ACS Synth. Biol. 2023, 12, 1, 153–163 | https://doi.org/10.1021/acssynbio.2c00426
Using enzymes to tame nitrogen-centred radicals for enantioselective hydroamination
Yuxuan Ye, Jingzhe Cao, Daniel G Oblinsky, Deeptak Verma, Christopher K Prier, Gregory D Scholes, Todd K Hyster
Nature Chemistry (2022) | https://doi.org/10.1038/s41557-022-01083-z
Similarity based enzymatic retrosynthesis
Karthik Sankaranarayanan, Esther Heid, Connor W. Coley, Deeptak Verma, William H. Green and Klavs F. Jensen
Chem. Sci., 2022, 13, 6039-6053 | DOI: 10.1039/D2SC01588A
Diverse Catalytic Reactions for the Stereoselective Synthesis of Cyclic Dinucleotide MK-1454
T Benkovics, F Peng, EM Phillips, C An, RS Bade, CK. Chung, ZEX Dance, PS Fier, JH Forstater, Z Liu, Z Liu, PE Maligres, NM Marshall, NS Marzijarani, JA McIntosh, SP Miller, JC Moore, AJ Neel, JV Obligacion, W Pan, MT Pirnot, M Poirier, M Reibarkh, BD Sherry, ZJ Song, L Tan, BWH Turnbull, D Verma, JH Waldman, L Wang, T Wang, MS Winston, and F Xu
Journal of the American Chemical Society 2022 144 (13), 5855-5863 DOI: 10.1021/jacs.1c12106
Successive remodeling of IgG glycans using a solid-phase enzymatic platform
Yen-Pang Hsu, Deeptak Verma, Shuwen Sun, Caroline McGregor, Ian Mangion, Benjamin F. Mann
Communications Biology, volume 5, 328 (2022)
https://www.nature.com/articles/s42003-022-03257-4
A kinase-cGAS cascade to synthesize a therapeutic STING activator
JA McIntosh, Z Liu, BM Andresen, NS Marzijarani, JC Moore, NM Marshall, M Borra-Garske, JV Obligacion, PS Fier, F Peng, JH Forstater, MS Winston, C An, W Chang, J Lim, MA Huffman, SP Miller, F Tsay, MD Altman, CA Lesburg, D Steinhuebel, B Trotter, JN Cumming, A Northrup, X Bu, BF Mann, M Biba, K Hiraga, GS Murphy, JN Kolev, A Makarewicz, W Pan, I Farasat, RS Bade, K Stone, D Duan, O Alvizo, D Adpressa, E Guetschow, E Hoyt, EL Regalado, S Castro, N Rivera, JP Smith, F Wang, A Crespo, D Verma, S Axnanda, ZEX Dance, PN Devine, D Tschaen, KA Canada, PG Bulger, BD Sherry, MD Truppo, RT Ruck, LC Campeau, DJ Bennett, GR Humphrey, KR Campos, ML Maddess (2022)
Nature 2022, v603, p439–444. https://doi.org/10.1038/s41586-022-04422-9
Engineered Ribosyl-1-Kinase Enables Concise Synthesis of Molnupiravir, an Antiviral for COVID-19
John A. McIntosh, Tamas Benkovics, Steven M. Silverman, Mark A. Huffman, Jongrock Kong, Peter E. Maligres, Tetsuji Itoh, Hao Yang, Deeptak Verma, Weilan Pan, Hsing-I Ho, Jonathan Vroom, Anders M. Knight, Jessica A. Hurtak, Artis Klapars, Anna Fryszkowska, William J. Morris, Neil A. Strotman, Grant S. Murphy, Kevin M. Maloney, and Patrick S. Fier (2021)
ACS-Central Science 2021, https://doi.org/10.1021/acscentsci.1c00608
Building blocks and blueprints for bacterial autolysins
Spencer Mitchell, Deeptak Verma, Karl E. Griswold, Chris Bailey-Kellogg (2021)
PLoS Comp Bio 17(4):e1008889 (2021) | https://doi.org/10.1371/journal.pcbi.1008889
Enantioselective Enzymatic Reduction of Acrylic Acids
Chihui An, Megan H. Shaw, Annika Tharp, Deeptak Verma, Hongming Li, Heather Wang, and Xiao Wang (2020)
ACS-Organic Letters 2020 | https://doi.org/10.1021/acs.orglett.0c02959
Globally deimmunized lysostaphin evades human immune surveillance and enables highly efficacious repeat dosing
Hongliang Zhao, Seth A. Brooks, Susan Eszterhas, Spencer Heim, Liang Li, Yan Q. Xiong, Yongliang Fang, Jack R. Kirsch, Deeptak Verma, Chris Bailey-Kellogg, Karl E. Griswold (2020)
Science Advances Vol. 6, no. 36, eabb9011 (2020)| DOI: 10.1126/sciadv.abb9011
Deep Dive into Machine Learning Models for Protein Engineering
Yuting Xu*, Deeptak Verma*, Robert P. Sheridan, Andy Liaw, Junshui Ma, Nicholas M. Marshall, John McIntosh, Edward C. Sherer, Vladimir Svetnik, Jennifer M. Johnston (2020)
*co-first author
ACS-JCIM (2020) | https://doi.org/10.1021/acs.jcim.0c00073
Design of an in vitro biocatalytic cascade for the manufacture of islatravir
Mark A. Huffman, Anna Fryszkowska, Oscar Alvizo, Margie Borra-Garske, Kevin R. Campos, Keith A. Canada, Paul N. Devine, Da Duan, Jacob H. Forstater, Shane T. Grosser, Holst M. Halsey, Gregory J. Hughes, Junyong Jo, Leo A. Joyce, Joshua N. Kolev, Jack Liang, Kevin M. Maloney, Benjamin F. Mann, Nicholas M. Marshall, Mark McLaughlin, Jeffrey C. Moore, Grant S. Murphy, Christopher C. Nawrat, Jovana Nazor, Scott Novick, Niki R. Patel, Agustina Rodriguez-Granillo, Sandra A. Robaire, Edward C. Sherer, Matthew D. Truppo, Aaron M. Whittaker, Deeptak Verma, Li Xiao, Yingju Xu, Hao Yang (2019)
Science 2019, Vol. 366, Issue 6470, pp. 1255-1259
Characterization of potent RSV neutralizing antibodies isolated from human memory B cells and identification of diverse RSV/hMPV cross-neutralizing epitopes
Xiao X, Tang A, Cox K, Wen Z, Callahan C, Sullivan N, Nahas D, Cosmi S, Galli J, Minnier M, Verma D, Babaoglu K, Su H, Bett A, Vora K, Chen Z, Zhang L (2019)
mAbs 2019, Nov-Dec; Vol. 11(8):1415-1427
Pareto optimization of combinatorial mutagenesis libraries.
Verma D, Grigoryan G, Bailey-Kellogg C (2018)
IEEE/ACM Trans Comput Biol Bioinform. Jul-Aug; Vol. 16(4):1143-1153
Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen.
Lai J, Verma D, Bailey-Kellogg C, Ackerman M (2018)
PEDS, Volume 31, Issue 4, p. 121–133.
Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity.
Salvat R, Verma D, Parker AS, Kirsch JR, Brooks SA, Bailey-Kellogg C, Griswold KE (2017)
PNAS, 114 (26) E5085-E5093.
EpiSweep: Computationally-driven reengineering of therapeutic proteins to reduce immunogenicity while maintaining function.
Choi Y*, Verma D*, Griswold KE, Bailey-Kellogg C (2017)
Computational Protein Design Meth Mol Bio,1529:375-398.
OCoM-SOCoM: Combinatorial mutagenesis library design optimally combining sequence and structure information.
Verma D, Grigoryan G, Bailey-Kellogg C (2016)
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 307-316.
Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in HLA-transgenic mice.
Zhao H, Verma D, Li W, Choi Y, Ndong C, Fiering SN, Bailey-Kellogg C, Griswold KE (2015)
Chemistry and Biology, 22(6):629-39.
Structure-based design of combinatorial mutagenesis libraries.
Verma D, Grigoryan G, Bailey-Kellogg C (2015)
Protein Science, 24(5):895-908.
Thermodynamic stability and flexibility characteristics of antibody fragment complexes.
Li T, Verma D, Tracka MB, Casas-Finet J, Livesay DR, Jacobs DJ (2014)
Protein Peptide Letters, 21(8):752-65.
A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.
Brown M, Verma D, Russell C, Jacobs DJ, Livesay DR (2014)
Protein Dynamics: Methods in Molecular Biology, 1084:227-38.
Towards comprehensive analysis of protein family quantitative stability-flexibility relationships using homology models.
Verma D, Jacobs DJ, Guo J, Livesay DR (2014)
Protein Dynamics: Methods in Molecular Biology, 1084:239-54.
Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity.
Verma D, Jacobs DJ, Livesay DR (2013)
PLoS Computational Biology, 9(7):e1003155
A visual analytics approach for exploring protein flexibility subspaces.
Barlowe S, Yang J, Jacobs DJ, Livesay DR, Alsakran J, Zhao Y, Verma D, Mottonen J (2013)
PacificVis, 193-200.
Changes in lysozyme flexibility upon mutation are frequent, large and long-ranged.
Verma D, Jacobs DJ, Livesay DR (2012)
PLoS Computational Biology, 8:e1002409
Ensemble properties of network rigidity reveal allosteric mechanisms.
Jacobs DJ, Livesay DR, Mottonen JM, Vorov OK, Istomin AY, Verma D (2012)
Methods in Molecular Biology, 796:279-304.
WaveMap: Interactively discovering features from protein flexibility matrices using wavelet-based visual analytics.
Barlow S, Liu Y, Yang J, Livesay DR, Jacobs DJ, Mottonen J, Verma D (2011)
Computer Graphics Forum, 30:1001-1010.
Predicting the melting point of human c-type lysozyme mutants.
Verma D, Jacobs DJ, Livesay DR (2010)
Current Protein and Peptide Science, 11:562-572.
Docking, MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogs.
Sengupta D, Verma D, Naik PK (2008)
In-Silico Biology, 8, 0023.
Docking Mode of Delvardine and its analogues into P66 domain oh HIV-1 Reverse Transcriptase: Screening using MM-GB/SA and ADME Screening.
Sengupta D, Verma D, Naik PK (2007)
Journal of Biosciences, 32 (7):1307-16
Comparative analysis of MMFF94x and AMBER99 using different protein class data sets: Aspartic Proteases, Serine Proteases, Metallo-Proteases and Sugar-Binding Proteins.
Singh H, Marla S, Verma D (2007)
Online Journal of Bioinformatics, 8(1): 45-55.
The binding modes, binding affinities and ADME screening of HIV-1 NNRTI inhibitor: Efavirnez and its analogs.
Sengupta D, Verma D, Naik PK (2007)
Online Journal of Bioinformatics, 8(1): 99-114.
Clustering of HIV-I subtype: Study of molecular diversity using phylogenetic analysis.
Sengupta D, Verma D, Mishra VS, Naik PK (2006)
Bioinformatics Trends (1), 1-12.
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