Author

D. Kihara

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 2 Biophysics· 2 Cell Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Assay:cryo-EM· 3 Approach:experimental assay· 3 Organism:human· 3 Approach:deep learning· 2 Research Focus:protein structure prediction· 2 Assay:proteomics· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

D. Sarkar· 3 shared G. Terashi· 3 shared A. Perez· 2 shared A. Singharoy· 2 shared M. Shekhar· 2 shared A. De La Fuente· 1 shared A. Kryshtafovych· 1 shared A. Mondal· 1 shared

Activity by Year

2018-2021 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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3 shared papersCell Biology

D. Sarkar

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

S. Jain, G. Uritskiy, M. Mahalingam, H. Batra, S. Chand, H. Trinh, C. Beck, W.-H. Shin, W. AlSalmi, G. Kijak, L. A. Eller, J. Kim, D. Kihara, S. Tovanabutra, G. Ferrari, , V. B. Rao

The paper identifies a genetic shift in an HIV-1 transmitted/founder virus that leads to broader antibody responses by altering the V2 domain structure.

bioRxiv · Jun 16, 2021Microbiology

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning

X. Wang, E. Alnabati, T. W. Aderinwale, S. R. Maddhuri Venkata Subramaniya, G. Terashi, D. Kihara

Emap2sec+ uses deep learning to detect DNA/RNA and protein secondary structures in intermediate-resolution cryo-EM maps, showing improved accuracy over its previous version.

bioRxiv · Aug 22, 2020 · PreprintBiophysics

Specific OCRL1 patient mutations differentially impact Lowe Syndrome cellular phenotypes

S. Ramadesikan, L. Skiba, J. Lee, K. Madhivanan, D. Sarkar, A. De La Fuente, C. B. Hanna, T. Hazbun, D. Kihara, R. C. Aguilar

This study shows how different OCRL1 mutations affect Lowe Syndrome cellular phenotypes and introduces a conformational disease mechanism.

bioRxiv · Aug 4, 2020Cell Biology

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, G. Debussche, N. Sisco, J. Nguyen, A. Mondal, J. Zook, J. Vant, P. Fromme, W. D. van Horn, D. Kihara, E. Tajkhorshid, K. Dill, , A. Singharoy

CryoFold determines protein structures from electron density maps using molecular dynamics and physical knowledge, producing ensembles of low-energy conformations validated experimentally.

bioRxiv · Aug 3, 2020 · PreprintBiophysics

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

C. L. Lawson, A. Kryshtafovych, P. D. Adams, P. Afonine, M. L. Baker, B. A. Barad, P. Bond, T. Burnley, R. Cao, J. Cheng, G. Chojnowski, K. Cowtan, K. A. Dill, F. DiMaio, D. Farrell, , Wan

The paper evaluates cryo-EM model quality using benchmark maps, showing high accuracy and reproducibility across 13 teams and recommending multiple metrics for model assessment.

bioRxiv · Jun 12, 2020Biochemistry

Kinetic And Structural Parameters Governing Fic-Mediated Adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78

S. Mattoo, A. Sanyal, E. A. Zbornik, B. G. Watson, C. Christoffer, J. Ma, D. Kihara

This study investigates the kinetic and structural parameters of HYPE-mediated adenylylation/AMPylation of BiP/GRP78, revealing site-specific effects on ATPase activity and substrate recognition.

bioRxiv · Dec 13, 2018Biochemistry