Current Opinion in Structural Biology 
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Curr Opin Struct Biol. 2024 Apr 24;86:102794. doi: 10.1016/j.sbi.2024.102794. Online ahead of print.ABSTRACTEngineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called 'de novo' design problem have recently been brought forward by developments in artificial intelligence. Generative architectures, such as language models and diffusion processes, seem adept at generating novel, yet realistic proteins that display desirable properties and perform specified functions. State-of-the-art design proto...
Source: Current Opinion in Structural Biology - April 25, 2024 Category: Biology Authors: Adam Winnifrith Carlos Outeiral Brian L Hie Source Type: research
Confronting heterogeneity in cryogenic electron microscopy data: Innovative strategies and future perspectives with data-driven methods
Curr Opin Struct Biol. 2024 Apr 23;86:102815. doi: 10.1016/j.sbi.2024.102815. Online ahead of print.ABSTRACTThe surge in the influx of data from cryogenic electron microscopy (cryo-EM) experiments has intensified the demand for robust algorithms capable of autonomously managing structurally heterogeneous datasets. This presents a wealth of exciting opportunities from a data science viewpoint, inspiring the development of numerous innovative, application-specific methods, many of which leverage contemporary data-driven techniques. However, addressing the challenges posed by heterogeneous datasets remains a paramount yet unr...
Source: Current Opinion in Structural Biology - April 24, 2024 Category: Biology Authors: Dari Kimanius Johannes Schwab Source Type: research
Investigations of membrane protein interactions in cells using fluorescence microscopy
Curr Opin Struct Biol. 2024 Apr 21;86:102816. doi: 10.1016/j.sbi.2024.102816. Online ahead of print.ABSTRACTThe interactions between proteins in membranes govern many cellular functions. Our ability to probe for such interactions has greatly evolved in recent years due to the introduction of new fluorescence techniques. As a result, we currently have a choice of methods that can be used to assess the spatial distribution of a membrane protein, its association state, and the thermodynamic stability of the oligomers in the native milieu. These biophysical measurements have revealed new insights into important biological proc...
Source: Current Opinion in Structural Biology - April 22, 2024 Category: Biology Authors: Mahmoud Abouelkheir Tanaya Roy Mateusz A Krzyscik Ece Özdemir Kalina Hristova Source Type: research
Investigations of membrane protein interactions in cells using fluorescence microscopy
Curr Opin Struct Biol. 2024 Apr 21;86:102816. doi: 10.1016/j.sbi.2024.102816. Online ahead of print.ABSTRACTThe interactions between proteins in membranes govern many cellular functions. Our ability to probe for such interactions has greatly evolved in recent years due to the introduction of new fluorescence techniques. As a result, we currently have a choice of methods that can be used to assess the spatial distribution of a membrane protein, its association state, and the thermodynamic stability of the oligomers in the native milieu. These biophysical measurements have revealed new insights into important biological proc...
Source: Current Opinion in Structural Biology - April 22, 2024 Category: Biology Authors: Mahmoud Abouelkheir Tanaya Roy Mateusz A Krzyscik Ece Özdemir Kalina Hristova Source Type: research
How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms
Curr Opin Struct Biol. 2024 Apr 16;86:102814. doi: 10.1016/j.sbi.2024.102814. Online ahead of print.ABSTRACTMolecular simulations are an essential asset in the first steps of drug design campaigns. However, the requirement of high-throughput limits applications mainly to qualitative approaches with low computational cost, but also low accuracy. Unlocking the potential of more rigorous quantum mechanical/molecular mechanics (QM/MM) models combined with molecular dynamics-based free energy techniques could have a tremendous impact. Indeed, these two relatively old techniques are emerging as promising methods in the field. Th...
Source: Current Opinion in Structural Biology - April 17, 2024 Category: Biology Authors: Giulia Rossetti Davide Mandelli Source Type: research
Apprehensions and emerging solutions in ML-based protein structure prediction
Curr Opin Struct Biol. 2024 Apr 16;86:102819. doi: 10.1016/j.sbi.2024.102819. Online ahead of print.ABSTRACTThe three-dimensional structure of proteins determines their function in vital biological processes. Thus, when the structure is known, the molecular mechanism of protein function can be understood in more detail and obtained information utilized in biotechnological, diagnostics, and therapeutic applications. Over the past five years, machine learning (ML)-based modeling has pushed protein structure prediction to the next level with AlphaFold in the front line, predicting the structure for hundreds of millions of pro...
Source: Current Opinion in Structural Biology - April 17, 2024 Category: Biology Authors: K äthe M Dahlström Tiina A Salminen Source Type: research
How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms
Curr Opin Struct Biol. 2024 Apr 16;86:102814. doi: 10.1016/j.sbi.2024.102814. Online ahead of print.ABSTRACTMolecular simulations are an essential asset in the first steps of drug design campaigns. However, the requirement of high-throughput limits applications mainly to qualitative approaches with low computational cost, but also low accuracy. Unlocking the potential of more rigorous quantum mechanical/molecular mechanics (QM/MM) models combined with molecular dynamics-based free energy techniques could have a tremendous impact. Indeed, these two relatively old techniques are emerging as promising methods in the field. Th...
Source: Current Opinion in Structural Biology - April 17, 2024 Category: Biology Authors: Giulia Rossetti Davide Mandelli Source Type: research
Apprehensions and emerging solutions in ML-based protein structure prediction
Curr Opin Struct Biol. 2024 Apr 16;86:102819. doi: 10.1016/j.sbi.2024.102819. Online ahead of print.ABSTRACTThe three-dimensional structure of proteins determines their function in vital biological processes. Thus, when the structure is known, the molecular mechanism of protein function can be understood in more detail and obtained information utilized in biotechnological, diagnostics, and therapeutic applications. Over the past five years, machine learning (ML)-based modeling has pushed protein structure prediction to the next level with AlphaFold in the front line, predicting the structure for hundreds of millions of pro...
Source: Current Opinion in Structural Biology - April 17, 2024 Category: Biology Authors: K äthe M Dahlström Tiina A Salminen Source Type: research
Emerging structure-based computational methods to screen the exploding accessible chemical space
Curr Opin Struct Biol. 2024 Apr 10;86:102812. doi: 10.1016/j.sbi.2024.102812. Online ahead of print.ABSTRACTStructure-based virtual screening can be a valuable approach to computationally select hit candidates based on their predicted interaction with a protein of interest. The recent explosion in the size of chemical libraries increases the chances of hitting high-quality compounds during virtual screening exercises but also poses new challenges as the number of chemically accessible molecules grows faster than the computing power necessary to screen them. We review here two novel approaches rapidly gaining in popularity ...
Source: Current Opinion in Structural Biology - April 11, 2024 Category: Biology Authors: Corentin Bedart Conrad Veranso Simoben Matthieu Schapira Source Type: research
Emerging structure-based computational methods to screen the exploding accessible chemical space
Curr Opin Struct Biol. 2024 Apr 10;86:102812. doi: 10.1016/j.sbi.2024.102812. Online ahead of print.ABSTRACTStructure-based virtual screening can be a valuable approach to computationally select hit candidates based on their predicted interaction with a protein of interest. The recent explosion in the size of chemical libraries increases the chances of hitting high-quality compounds during virtual screening exercises but also poses new challenges as the number of chemically accessible molecules grows faster than the computing power necessary to screen them. We review here two novel approaches rapidly gaining in popularity ...
Source: Current Opinion in Structural Biology - April 11, 2024 Category: Biology Authors: Corentin Bedart Conrad Veranso Simoben Matthieu Schapira Source Type: research
Emerging structure-based computational methods to screen the exploding accessible chemical space
Curr Opin Struct Biol. 2024 Apr 10;86:102812. doi: 10.1016/j.sbi.2024.102812. Online ahead of print.ABSTRACTStructure-based virtual screening can be a valuable approach to computationally select hit candidates based on their predicted interaction with a protein of interest. The recent explosion in the size of chemical libraries increases the chances of hitting high-quality compounds during virtual screening exercises but also poses new challenges as the number of chemically accessible molecules grows faster than the computing power necessary to screen them. We review here two novel approaches rapidly gaining in popularity ...
Source: Current Opinion in Structural Biology - April 11, 2024 Category: Biology Authors: Corentin Bedart Conrad Veranso Simoben Matthieu Schapira Source Type: research
Emerging structure-based computational methods to screen the exploding accessible chemical space
Curr Opin Struct Biol. 2024 Apr 10;86:102812. doi: 10.1016/j.sbi.2024.102812. Online ahead of print.ABSTRACTStructure-based virtual screening can be a valuable approach to computationally select hit candidates based on their predicted interaction with a protein of interest. The recent explosion in the size of chemical libraries increases the chances of hitting high-quality compounds during virtual screening exercises but also poses new challenges as the number of chemically accessible molecules grows faster than the computing power necessary to screen them. We review here two novel approaches rapidly gaining in popularity ...
Source: Current Opinion in Structural Biology - April 11, 2024 Category: Biology Authors: Corentin Bedart Conrad Veranso Simoben Matthieu Schapira Source Type: research
CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation
Curr Opin Struct Biol. 2024 Apr 9;86:102813. doi: 10.1016/j.sbi.2024.102813. Online ahead of print.ABSTRACTOxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers a...
Source: Current Opinion in Structural Biology - April 10, 2024 Category: Biology Authors: Turner P Brown Dane E Santa Brett A Berger Lingyang Kong Nathan J Wittenberg Wonpil Im Source Type: research
Emerging strategies for prospective discovery of molecular glue degraders
Curr Opin Struct Biol. 2024 Apr 9;86:102811. doi: 10.1016/j.sbi.2024.102811. Online ahead of print.ABSTRACTMolecular glue (MG) degraders are monovalent small molecule compounds that co-opt E3 ubiquitin ligases to target neo-substrates for proteasomal degradation. Here, we provide a concise review of recent advances in rational MG discovery, which are categorized into two major strategies, ligand modification and de novo discovery. We also highlight the structural mechanisms underlying the formation of MG-enabled ternary complexes and their thermodynamic properties. Finally, we summarize the broader category of proximity in...
Source: Current Opinion in Structural Biology - April 10, 2024 Category: Biology Authors: Baiyun Wang Shiyun Cao Ning Zheng Source Type: research
CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation
Curr Opin Struct Biol. 2024 Apr 9;86:102813. doi: 10.1016/j.sbi.2024.102813. Online ahead of print.ABSTRACTOxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers a...
Source: Current Opinion in Structural Biology - April 10, 2024 Category: Biology Authors: Turner P Brown Dane E Santa Brett A Berger Lingyang Kong Nathan J Wittenberg Wonpil Im Source Type: research
