Brian D. Ratnasinghe
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View article: A Multi-State Structural Genomics Approach Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases
A Multi-State Structural Genomics Approach Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases Open
Purpose Genetic variation in ATP Binding Cassette Subfamily C Member 6 (ABCC6) can cause both pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI). Despite both diseases being rare, there are already 930 …
View article: Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction
Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction Open
Artificial Intelligence (AI)-based deep learning methods for predicting protein structures are reshaping knowledge development and scientific discovery. Recent large-scale application of AI models for protein structure prediction has chang…
View article: RAG genomic variation causes autoimmune diseases through specific structure-based mechanisms of enzyme dysregulation
RAG genomic variation causes autoimmune diseases through specific structure-based mechanisms of enzyme dysregulation Open
Interpreting genetic changes observed in individual patients is a critical challenge. The array of immune deficiency syndromes is typically caused by genetic variation unique to individuals. Therefore, new approaches are needed to interpre…
View article: Beyond Structural Bioinformatics for Genomics with Dynamics Characterization of an Expanded KRAS Mutational Landscape
Beyond Structural Bioinformatics for Genomics with Dynamics Characterization of an Expanded KRAS Mutational Landscape Open
Current capabilities in genomic sequencing outpace functional interpretations. Our previous work showed that 3D protein structure calculations enhance mechanistic understanding of genetic variation in sequenced tumors and patients with rar…
View article: Beyond structural bioinformatics for genomics with dynamics characterization of an expanded KRAS mutational landscape
Beyond structural bioinformatics for genomics with dynamics characterization of an expanded KRAS mutational landscape Open
Current capabilities in genomic sequencing outpace functional interpretations. Our previous work showed that 3D protein structure calculations enhance mechanistic understanding of genetic variation in sequenced tumors and patients with rar…
View article: Ion Binding to the bcl-2 G-Quadruplex from Polarizable Simulations with the Drude Force Field
Ion Binding to the bcl-2 G-Quadruplex from Polarizable Simulations with the Drude Force Field Open
View article: Ion Binding Properties and Dynamics of the <i>bcl-</i>2 G-Quadruplex Using a Polarizable Force Field
Ion Binding Properties and Dynamics of the <i>bcl-</i>2 G-Quadruplex Using a Polarizable Force Field Open
G-quadruplexes (GQs) are topologically diverse, highly thermostable noncanonical nucleic acid structures that form in guanine-rich sequences in DNA and RNA. GQs are implicated in transcriptional and translational regulation and genome main…
View article: Polarization Molecular Dynamics of an RNA DUPLEX:G-quadruplex Junction in Complex with the Fragile X Mental Retardation Protein
Polarization Molecular Dynamics of an RNA DUPLEX:G-quadruplex Junction in Complex with the Fragile X Mental Retardation Protein Open
View article: Structure and Dynamics of the Bcl-2 Promoter G-Quadruplex using the Drude Polarizable Force Field
Structure and Dynamics of the Bcl-2 Promoter G-Quadruplex using the Drude Polarizable Force Field Open
View article: Nucleic Acid Dynamics
Nucleic Acid Dynamics Open
This project includes simulations of DNA and RNA using the Drude polarizable and CHARMM36 non-polarizable force fields.