Exploring the ability of the MD+ FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data
Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and
antibody-based therapies. The ability to predict these escape mutations with computer …
antibody-based therapies. The ability to predict these escape mutations with computer …
Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability
Background Computational methods of predicting protein stability changes upon missense
mutations are invaluable tools in high-throughput studies involving a large number of protein …
mutations are invaluable tools in high-throughput studies involving a large number of protein …
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA. 2.86 Spike Protein with …
N Raisinghani, M Alshahrani, G Gupta… - Journal of Chemical …, 2024 - ACS Publications
The latest wave of SARS-CoV-2 Omicron variants displayed a growth advantage and
increased viral fitness through convergent evolution of functional hotspots that work …
increased viral fitness through convergent evolution of functional hotspots that work …
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1
AE Ali, LL Li, MJ Courtney… - Briefings in …, 2024 - academic.oup.com
De novo mutations in the synaptic GTPase activating protein (SynGAP) are associated with
neurological disorders like intellectual disability, epilepsy, and autism. SynGAP is also …
neurological disorders like intellectual disability, epilepsy, and autism. SynGAP is also …
Molecular modeling predicts novel antibody escape mutations in the respiratory syncytial virus fusion glycoprotein
SS Beach, MKA Hull, FM Ytreberg, JS Patel… - Journal of …, 2022 - Am Soc Microbiol
Monoclonal antibodies are increasingly used for the prevention and/or treatment of viral
infections. One caveat of their use is the ability of viruses to evolve resistance to antibody …
infections. One caveat of their use is the ability of viruses to evolve resistance to antibody …
Atomistic simulations and in silico mutational profiling of protein stability and binding in the SARS-CoV-2 spike protein complexes with nanobodies: Molecular …
GM Verkhivker, S Agajanian, DY Oztas, G Gupta - ACS omega, 2021 - ACS Publications
Structure-functional studies have recently revealed a spectrum of diverse high-affinity
nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience …
nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience …
The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6
SARS-CoV-2 is the pathogen responsible for COVID-19 that has claimed over six million
lives as of July 2022. The severity of COVID-19 motivates a need to understand how it could …
lives as of July 2022. The severity of COVID-19 motivates a need to understand how it could …
An optimized thermodynamics integration protocol for identifying beneficial mutations in antibody design
Accurate identification of beneficial mutations is central to antibody design. Many knowledge-
based (KB) computational approaches have been developed to predict beneficial mutations …
based (KB) computational approaches have been developed to predict beneficial mutations …
In silico energetic and molecular dynamic simulations studies demonstrate potential effect of the point mutations with implications for protein engineering in BDNF
VMD Darshan, N Arumugam, AI Almansour… - International Journal of …, 2024 - Elsevier
Protein engineering by directed evolution is time-consuming. Hence, in silico techniques like
FoldX-Yasara for∆∆ G calculation, and SNPeffect for predicting propensity for aggregation …
FoldX-Yasara for∆∆ G calculation, and SNPeffect for predicting propensity for aggregation …
Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have
originated from a bat species, can infect a wide range of non-human hosts. Bats are known …
originated from a bat species, can infect a wide range of non-human hosts. Bats are known …