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Discovery of novel Akt1 inhibitors by an ensemble-based virtual screening method, molecular dynamics simulation, and in vitro biological activity testing
Akt1, as an important member of the Akt family, plays a controlled role in cancer cell growth and survival. Inhibition of Akt1 activity can promote...
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Curb your enthusiasm for explaining the complexity of landscape configurations in terms of thermodynamics
ContextSeveral studies have explored using Boltzmann entropy to quantify the configurational complexity of landscapes. Additionally, these studies...
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Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach
BackgroundProtein-DNA interaction governs a large number of cellular processes, and it can be altered by a small fraction of interface residues,...
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Develo** Complex RNA Design Applications in the Infrared Framework
Applications in biotechnology and bio-medical research call for effective strategies to design novel RNAs with very specific properties. Such...
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RNA Secondary Structure Thermodynamics
Several different ways to predict RNA secondary structures have been suggested in the literature. Statistical methods, such as those that utilize...
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Modified Nucleotides and RNA Structure Prediction
Nucleotide modifications are occurrent in all types of RNA and play an important role in RNA structure formation and stability. Modified bases not...
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Molecular simulations by generalized-ensemble algorithms in isothermal–isobaric ensemble
Generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The...
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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various...
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On an enhancement of RNA probing data using information theory
Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance...
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Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections
We illustrate three methods for calculating the binodals of phase-separated condensates from molecular simulations. Because molecular simulations can...
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RNA secondary structure packages evaluated and improved by high-throughput experiments
Despite the popularity of computer-aided study and design of RNA molecules, little is known about the accuracy of commonly used structure modeling...
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Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach
Breast cancer remains a major public health challenge worldwide. The identification of accurate biomarkers is critical for the early detection and...
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Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers
Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons...
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All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations
Protein aggregates are associated with more than 40 serious human diseases. To understand the formation mechanism of protein aggregates at atomic...
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Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory
BackgroundThe nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure...
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Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under...
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Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases....
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Targeting AFP-RARβ complex formation: a potential strategy for treating AFP-positive hepatocellular carcinoma
Alpha-fetoprotein (AFP) is a glycoprotein primarily expressed during embryogenesis, with declining levels postnatally. Elevated AFP levels correlate...
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The maximum entropy principle to predict forager spatial distributions: an alternate perspective for movement ecology
The Maximum Entropy (MaxEnt) principle is a powerful inference principle which enables the determination of the distribution of a system, on the...
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Knowledge-Based Unfolded State Model for Protein Design
The design of proteins and miniproteins is an important challenge. Designed variants should be stable, meaning the folded/unfolded free energy...