ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLocal structural order and molecular associations in water-DMSO mixtures. Molecular dynamics studyIosif I. Vaisman Max L. BerkowitzCite this: J. Am. Chem. Soc. 1992, 114, 20, 7889–7896Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ja00046a038https://doi.org/10.1021/ja00046a038research-articleACS PublicationsRequest reuse permissionsArticle...

Abstract Motivation: Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into structure and function. Such are also valuable design engineering new proteins. Previously described methods have utilized properties sequence or to predict free energy change mutants due thermal (ΔΔG) denaturant (ΔΔGH2O) denaturations, as well mutant (ΔTm), through application either computational energy-based approaches machine learning techniques....

There is a considerable literature on the source of thermostability proteins from thermophilic organisms. Understanding mechanisms for this would provide insights into generally and permit design synthetic hyperstable biocatalysts. We have systematically tested large number sequence structure derived quantities their ability to discriminate thermostable non-thermostable orthologs using sets mesophile-thermophile ortholog pairs. Most correspond properties previously reported be associated...

Delaunay tessellation is applied for the first time in analysis of protein structure. By representing amino acid residues chains by Cα atoms, described as a set points three-dimensional space. structure generates an aggregate space-filling irregular tetrahedra, or simplices. The vertices each simplex define objectively four nearest neighbor i.e., nearest-neighbor residues. A classification scheme introduced which simplices are divided into five classes based on relative positions vertex...

Utilizing cutting-edge supervised classification and regression algorithms, three web-based tools have been developed for predicting stability changes upon single residue substitutions in proteins with known native structures. Trained models classify independent mutant test sets accuracies ranging from 87 to 94%. Attributes representing each protein are based on a computational mutagenesis methodology relying four-body statistical potential, illustrating novel integration of both...

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three the predictors evaluate protein stability mutation, each complementing distinct experimental approach. Two additional classifiers are available, one activity due replacements and other determining disease potential mutations associated...

Introduction Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics for combating plant pathogenic bacteria in agriculture and the environment. However, identifying potent AMPs through laborious experimental assays is resource-intensive time-consuming. To address these limitations, this study presents a bioinformatics approach utilizing machine learning models predicting selecting active against bacteria. Methods N-gram representations of peptide sequences with...

CD147, also known as extracellular matrix metalloproteinase inducer, is a regulator of production and serves signaling receptor for cyclophilins. Previously, we demonstrated that cell surface expression CD147 sensitive to cyclophilin-binding drug cyclosporin A, suggesting involvement cyclophilin in the regulation intracellular transport CD147. In this report, identify 60 (Cyp60), distinct member family proteins. co-immunoprecipitated with Cyp60, confocal immunofluorescent microscopy revealed...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDistance Dependence of Water Structure around Model SolutesIosif I. Vaisman, Frank K. Brown, and Alexander TropshaCite this: J. Phys. Chem. 1994, 98, 21, 5559–5564Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 1994https://pubs.acs.org/doi/10.1021/j100072a025https://doi.org/10.1021/j100072a025research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations55LEARN...

An important area of research in biochemistry and molecular biology focuses on characterization enzyme mutants. However, synthesis analysis experimental mutants is time consuming expensive. We describe a machine-learning approach for inferring the activity levels all unexplored single point an enzyme, based training set such with experimentally measured activity.Based Delaunay tessellation-derived four-body statistical potential function, perturbation vector measuring environmental changes...

Zeolites are microporous crystalline materials with highly regular framework structures consisting of molecular-sized pores and channels. The characteristic type a zeolite is conventionally defined by combining information on its coordination sequences, vertex symbols, tiling, transitivity information. Here we present novel knowledge-based approach for classification. We show the predicting abilities machine learning model that uses nine-dimensional feature vector including topological...

There is an urgent need for therapies that will reduce the mortality of patients with bone metastasis. In this study, we profiled protein signal pathway networks human metastasis microenvironment. The goal was to identify sets interacting proteins correlate survival time following first diagnosis metastasis.Using Reverse Phase Protein Microarray technology, measured expression 88 end points in microenvironment 159 tissue samples derived from primary carcinomas and sarcomas.Metastases...

Successful management of chronic human immunodeficiency virus type 1 (HIV-1) infection with a cocktail antiretroviral medications can be negatively affected by the presence drug resistant mutations in viral targets. These targets include HIV-1 protease (PR) and reverse transcriptase (RT) proteins, for which number inhibitors are available on market routinely prescribed. Protein mutational patterns associated varying degrees resistance to their respective inhibitors, extremes that range from...

Opioid receptors (OPRs) are the main targets for treatment of pain and related disorders. The opiate compounds that activate these effective analgesics but their use leads to adverse effects, they often highly addictive drugs abuse. There is an urgent need alternative chemicals reduce/avoid unwanted effects in order relieve public health crisis opioid addiction. Here, we aim develop computational models predict OPR activity small molecule based on chemical structures apply identify novel...

There is substantial interest in methods designed to predict the effect of nonsynonymous single nucleotide polymorphisms (nsSNPs) on protein function, given their potential relationship heritable diseases. Current state-of-the-art supervised machine learning algorithms, such as random forest (RF), train models that classify amino acid mutations proteins either neutral or deleterious function. However, it frequently case functional a polymorphism resides between these two extremes. The...

ApoB-100 is a member of large lipid transfer protein superfamily and one the main apolipoproteins found on low-density lipoprotein (LDL) very (VLDL) particles. Despite its clinical significance for development cardiovascular disease, there limited information apoB-100 structure. We have developed novel method based “divide conquer” algorithm, using PSIPRED software, by dividing into five subunits 11 domains. Models each domain were prepared I-TASSER, DEMO, RoseTTAFold, Phyre2, MODELLER....

The Delaunay tessellation of several sets real and simplified model protein structures has been used to explore graph theoretic properties residue contact networks. system contacts defined by residues joined edges in the simplices can be thought as a or network analyzed using techniques from elementary theory complex Such analysis indicates that networks have small world character, but technically are not This approach also formed native most misfolded decoys differentiated their respective...

Abstract A topological representation of proteins is developed that makes use two metrics: the Euclidean metric for identifying natural nearest neighboring residues via Delaunay tessellation in Cartesian space and distance between sequence space. Using this representation, we introduce a quantitative computationally inexpensive method comparison protein structural topology. The ultimately results numerical score quantifying heuristically defined properties scoring scheme are investigated...

HIV-1 targets human cells expressing both the CD4 receptor, which binds viral envelope glycoprotein gp120, as well either CCR5 (R5) or CXCR4 (X4) co-receptors, interact primarily with third hypervariable loop (V3 loop) of gp120. Determination affinity for R5 X4 co-receptor on host facilitates inclusion antagonists a part patient treatment strategies. A dataset 1193 distinct gp120 V3 peptide sequences (989 R5-utilizing, 204 X4-capable) is utilized to train predictive classifiers based...

In this work a structural characterization of zeolite crystals is performed by identifying the framework type to which each belongs. The assigned for 1433 database entries in FIZ/NIST Inorganic Crystal Structure Database (ICSD) populating 95 types. These correspond both natural and synthetic zeolites. Each ICSD entry based on published containing crystallographic information crystalline structure some physical chemical data. Today, Commission International Zeolite Association recognizes...