Center for Computational Biology Scholarly Works
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Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket
(American Chemical Society, 2023-01-27)Ligand binding thermodynamics and kinetics are critical parameters for drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics from molecular simulations due to ... -
Deep Boosted Molecular Dynamics: Accelerating Molecular Simulations with Gaussian Boost Potentials Generated Using Probabilistic Bayesian Deep Neural Network
(American Chemical Society, 2023-05-23)We have developed a new deep boosted molecular dynamics (DBMD) method. Probabilistic Bayesian neural network models were implemented to construct boost potentials that exhibit Gaussian distribution with minimized anharmonicity, ... -
Critical Non-Covalent Binding Intermediate for an Allosteric Covalent Inhibitor of SUMO E1
(American Chemical Society, 2023-03-10)Post-translational modifications by small ubiquitin-like modifiers (SUMOs) are dysregulated in many types of cancers. The SUMO E1 enzyme has recently been suggested as a new immuno-oncology target. COH000 was recently ... -
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
(Oxford University Press, 2023-07-05)Motivation Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. ... -
Identification of a novel transport system in Borrelia burgdorferi that links the inner and outer membranes
(Pathogens and Disease, 2023-06-29)Borrelia burgdorferi, the spirochete that causes Lyme disease, is a diderm organism that is similar to Gram-negative organisms in that it contains both an inner and outer membrane. Unlike typical Gram-negative organisms, ... -
Challenges and frontiers of computational modelling of biomolecular recognition
(Cambridge University Press, 2022-08-19)Biomolecular recognition including binding of small molecules, peptides and proteins to their target receptors plays a key role in cellular function and has been targeted for therapeutic drug design. However, the high ... -
Editorial: Protein recognition and associated diseases
(Frontiers Media, 2023-05-22) -
Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein
(Nature Research, 2023-02-14)Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease ... -
Towards a structurally resolved human protein interaction network
(Nature Research, 2023-01-23)Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their molecular mechanisms. However, fewer than 5% of hundreds of ... -
Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics
(eLife Sciences Publications, 2023-05-20)Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological ... -
Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search
(Nature Research, 2022-10-12)AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes ... -
GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes
(2022-06-15)Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function. The ... -
DOCKGROUND membrane protein-protein set
(Public Library of Science, 2022-05-17)Membrane proteins are significantly underrepresented in Protein Data Bank despite their essential role in cellular mechanisms and the major progress in experimental protein structure determination. Thus, computational ... -
Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives
(Dove Medical Press, 2021-02-20)Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular ... -
Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations
(Cell Press, 2021-03-19)Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin ... -
A clinically relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position
(Elsevier, 2020-11-09)Conventionally, most amino acid substitutions at “important” protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of nonconserved positions for which ... -
Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H
(Springer Nature, 2021-01-28)Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific ... -
Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor
(Frontiers Media, 2021-04-27)Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the ... -
Machine learning differentiates enzymatic and non-enzymatic metals in proteins
(Nature Research, 2021-06-17)Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is ... -
Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness
(American Society for Microbiology, 2019-11-12)Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in ...
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