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Showing 1 to 13 of 13 for “"Computational protein design"”.
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Methods and applications in computational protein design
… our work on applications and methods for computational protein design. First, we apply computational protein design to address the problem of degradation in stored proteins. Specifically, we target cysteine, asparagine, glutamine, and methionine amino acid residues to reduce or eliminate a …
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Exact rotamer optimization for computational protein design
… the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* …
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Multistate Computational Protein Design: Theories, Methods, and Applications
Traditional computational protein design (CPD) calculations model sequence perturbations and evaluate their stabilities using a single fixed protein backbone template in an approach referred to as single‐state design (SSD). However, certain design objectives require the explicit consideration of …
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Enhanced Potts Models for Improved Computational Protein Design
Proteins are the fundamental building blocks of life, contributing to the structure, function, and regulation of all living cells. The ability to computationally design proteins to serve specific functions is thus of particular interest to the bioengineering and biomedical fields. TERMinator is a …
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MULTIPLE STRATEGIES IN COMPUTATIONAL PROTEIN DESIGN: STRUCTURAL INTUITION, PROBABILISTIC INVERSE FOLDING, AND GENERATIVE APPROACHES
Designing proteins with specific structural and functional features has become increasingly feasible through the integration of physics-based modeling, statistical inference, and generative algorithms. This work presents conceptual, methodological, and applied examples spanning multiple stages of …
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Efficient New Computational Protein Design Algorithms, with Applications to Drug Resistance Prediction and HIV Antibody Design
<p>Proteins are essential for myriad biological functions, including DNA replication, molecular transport, catalysis, and antigen recognition. Protein function is determined by three dimensional structure, which is largely determined by amino acid composition. The functional diversity of known …
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Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing
<p>One of the key properties of proteins is that they exhibit remarkable affinities and specificities for small-molecule and peptide binding partners. To improve the success rate of rational, computational protein design and widen the scope of potential applications, it is useful to define …
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Computational approaches for the design and prediction of protein-protein interactions
There is a large class of applications in computational structural biology for which atomic-level representation is crucial for understanding the underlying biological phenomena, yet explicit atomic-level modeling is computationally prohibitive. Computational protein design, homology modeling, …
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De novo designed protein switches to enable increased specificity of targeted therapeutics
… are also expressed on healthy tissues. Using computational protein design, we developed colocalization- dependent switches which activate only on the surface of cells expressing a precise combination of antigens (Lajoie et al., 2020). We have shown that these designed protein switches are …
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Computational structure-based modeling and analysis with application to rational and evolutionary molecular engineering
The design and development of new proteins and small molecules has considerable practical application in medicine, industry, and basic science. Frequently, progress in this area is made by altering an existing small molecule or protein for new function. This thesis presents methods for the analysis …
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Computational design of functional cyclic peptides using deep learning
… mid-point between biologics and small molecules. Computational design of structured cyclic peptides has been successful using Rosetta, even design of membrane traversing cyclic peptides, but efforts to design binders to protein targets have led to only a handful of successful cases. Deep learning …
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In silico protein evolution by intelligent design: creating new and improved protein structures
Natural proteins perform a startling diversity of biological functions, but comprise a miniscule fraction of the theoretical sequence-structure space that polypeptides might occupy. The goal of protein design is to identify new free-energy minima in this sequence-structure landscape so as to expand …
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Molecular Simulation of Mutation Effects on Protein Folding and Function
The amino acid sequence of a protein encodes its folding, the reaction by which a peptide self-assembles into its native functional shape. A folded protein will then go on to carry on biological functions such as ligand binding, signaling, mechanical functions, or biomolecular catalysis. While much …