Vikram Khipple Mulligan
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Explore the profile of Vikram Khipple Mulligan including associated specialties, affiliations and a list of published articles.
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30
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1489
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Recent Articles
1.
Powers A, Renfrew P, Hosseinzadeh P, Mulligan V
bioRxiv
. 2025 Mar;
PMID: 40060652
Macrocycles are a promising therapeutic class. The incorporation of heterochiral and non-natural chemical building-blocks presents challenges for rational design, however. With no existing machine learning methods tailored for heterochiral macrocycle...
2.
Zhu Q, Mulligan V, Shasha D, Shasha D
bioRxiv
. 2024 Jul;
PMID: 39005429
Rational computational design is crucial to the pursuit of novel drugs and therapeutic agents. Meso-scale cyclic peptides, which consist of 7-40 amino acid residues, are of particular interest due to...
3.
Ertelt M, Mulligan V, Maguire J, Lyskov S, Moretti R, Schiffner T, et al.
PLoS Comput Biol
. 2024 Mar;
20(3):e1011939.
PMID: 38484014
Post-translational modifications (PTMs) of proteins play a vital role in their function and stability. These modifications influence protein folding, signaling, protein-protein interactions, enzyme activity, binding affinity, aggregation, degradation, and much...
4.
Dodd-O J, Acevedo-Jake A, Azizogli A, Mulligan V, Kumar V
Methods Mol Biol
. 2022 Nov;
2597:187-216.
PMID: 36374423
Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes. Shorter proteins,...
5.
Bhardwaj G, OConnor J, Rettie S, Huang Y, Ramelot T, Mulligan V, et al.
Cell
. 2022 Aug;
185(19):3520-3532.e26.
PMID: 36041435
We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6-12 residue macrocycles with a wide...
6.
Leman J, Lyskov S, Lewis S, Adolf-Bryfogle J, Alford R, Barlow K, et al.
Nat Commun
. 2021 Nov;
12(1):6947.
PMID: 34845212
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of...
7.
Maguire J, Grattarola D, Mulligan V, Klyshko E, Melo H
PLoS Comput Biol
. 2021 Sep;
17(9):e1009037.
PMID: 34570773
Graph representations are traditionally used to represent protein structures in sequence design protocols in which the protein backbone conformation is known. This infrequently extends to machine learning projects: existing graph...
8.
Hosseinzadeh P, Watson P, Craven T, Li X, Rettie S, Pardo-Avila F, et al.
Nat Commun
. 2021 Jun;
12(1):3384.
PMID: 34099674
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we...
9.
Mulligan V
Expert Opin Drug Discov
. 2021 May;
16(9):1025-1044.
PMID: 33993816
: Structure-guided drug discovery relies on accurate computational methods for modeling macromolecules. Simulations provide means of predicting macromolecular folds, of discovering function from structure, and of designing macromolecules to serve...
10.
Yachnin B, Mulligan V, Khare S, Bailey-Kellogg C
J Chem Inf Model
. 2021 Apr;
61(5):2368-2382.
PMID: 33900750
As non-"self" macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions. To enable the flexible...