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Protein-Protein Docking Methods and Protocols
This volume covers a wide array of topics on protein-protein docking ranging from the fundamentals of the method and its recent developments to...
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Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms,...
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Docking Foundations: From Rigid to Flexible Docking
Despite the development of methods for the experimental determination of protein structures, the dissonance between the number of known sequences and...
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From Multiple Protein Docking to Protein–Protein Docking at Interactome Level
Molecular docking is used to anticipate the optimal orientation of a particular molecule to a target to form a stable complex. It makes predictions...
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Approaches to Backbone Flexibility in Protein–Protein Docking
Proteins are the fundamental organic macromolecules in living systems that play a key role in a variety of biological functions including...
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Sampling and Scoring in Protein–Protein Docking
Protein–protein docking is considered one of the most important techniques supporting experimental proteomics. Recent developments in the field of...
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Software and Databases for Protein–Protein Docking
Protein–protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of...
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Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies
Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very...
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Assessment of Protein–Protein Docking Models Using Deep Learning
Protein–protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain...
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EasyDock: customizable and scalable docking tool
Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also...
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Protein-Protein Docking Approach to GPCR Oligomerization
G-protein-coupled receptors (GPCRs), the largest family of human membrane proteins, play a crucial role in cellular control and are the target of...
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Molecular Docking for Virtual Screening of Potential Active Ingredients in Chinese Medicines
Traditional Chinese medicine (TCM) plays a vital role in the prevention and treatment of various diseases for thousands of years. It is of great...
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Challenges of Protein-Protein Docking of the Membrane Proteins
Despite the recent advances in the determination of high-resolution membrane protein (MP) structures, the structural and functional characterization...
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Cobdock: an accurate and practical machine learning-based consensus blind docking method
Probing the surface of proteins to predict the binding site and binding affinity for a given small molecule is a critical but challenging task in...
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Assessing Protein-Protein Docking Protocols: Case Studies of G-Protein-Coupled Receptor Interactions
The interactions of G-protein-coupled receptors (GPCRs) with other proteins are critical in several cellular processes but resolving their structural...
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Molecular docking in organic, inorganic, and hybrid systems: a tutorial review
Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular...
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ChemFlow_py: a flexible toolkit for docking and rescoring
The design of accurate virtual screening tools is an open challenge in drug discovery. Several structure-based methods have been developed at...
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Molecular-docking electrolytes enable high-voltage lithium battery chemistries
Ideal rechargeable lithium battery electrolytes should promote the Faradaic reaction near the electrode surface while mitigating undesired side...
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Docking-Based Prediction of Peptide Binding to MHC Proteins
Major histocompatibility complex (MHC) proteins are the most polymorphic and polygenic proteins in humans. They bind peptides, derived from cleavage...
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Covalent docking in CDOCKER
Targeted covalent inhibitors (TCIs) are considered to be an important component in the toolbox of drug discovery and about 30% of currently marketed...
