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iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides.

Phasit Charoenkwan, Janchai Yana, Chanin Nantasenamat, Md Mehedi Hasan, Watshara Shoombuatong,

Umami or the taste of monosodium glutamate represents one of the major attractive taste modalities in humans. Therefore, knowledge about biophysical and biochemical properties of the umami taste is important for both scientific research and the food industry. Experimental approaches for predicting umami peptides are labor intensive, time consuming, and ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Identification of Noncompetitive Protein-Ligand Interactions for Structural Optimization.

Andreas Tosstorff, Jason C Cole, Robin Taylor, Seth F Harris, Bernd Kuhn,

For efficient structure-guided drug design, it is important to have an excellent understanding of the quality of interactions between the target receptor and bound ligands. Identification and characterization of poor intermolecular contacts offers the possibility to focus design efforts directly on ligand regions with suboptimal molecular recognition. To enable a ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search.

Chun Jiang Zhu, Minghu Song, Qinqing Liu, Chloé Becquey, Jinbo Bi,

Structurally similar analogues of given query compounds can be rapidly retrieved from chemical databases by the molecular similarity search approaches. However, the computational cost associated with the exhaustive similarity search of a large compound database will be quite high. Although the latest indexing algorithms can greatly speed up the search ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Atomic Partial Charges as Descriptors for Barrier Heights.

Malte Döntgen, Yann Fenard, K Alexander Heufer,

Atomic partial charges are found to be valuable descriptors for barrier heights of unimolecular reactions due to the considerable information about the electronic structure embedded in them. If the chemical changes of the reactions are somewhat centralized at a single atom, the respective partial charge is a potentially meaningful descriptor ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling.

Till Siebenmorgen, Martin Zacharias,

Accurate prediction and evaluation of protein-protein complex structures are of major importance to understand the cellular interactome. Typically, putative complexes are predicted based on docking methods, and simple force field or knowledge-based scoring functions are applied to evaluate single complex structures. We have extended a replica-exchange-based scheme employing different levels ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Structural and Dynamic Insights into Redundant Function of YTHDF Proteins.

Yaozong Li, Rajiv K Bedi, Elena V Moroz-Omori, Amedeo Caflisch,

Three YTH-domain family proteins (YTHDF1, YTHDF2, and YTHDF3) recognize the N6-methyladenosine (m6A) modification of mRNA in cells. However, the redundancy of their cellular functions has been disputed. We investigate their interactions with m6A-containing RNA using X-ray crystallography and molecular dynamics (MD). The new X-ray structures and MD simulations show that ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Converging Interests: Chemoinformatics, History, and Bibliometrics.

Wenxi Zhao, Dmitriy Korobskiy, Shreya Chandrasekharan, Kenneth M Merz, George Chacko,

Modern scientometric techniques, applied at scale, can provide valuable information that complements qualitative investigation of the accumulation of knowledge in a field. We discuss a trio of articles from computational chemistry selected from an analysis of 181 million tri-cited articles. ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Prediction of Molecular Electronic Transitions Using Random Forests.

Beomchang Kang, Chaok Seok, Juyong Lee,

Fluorescent molecules, fluorophores or dyes, play essential roles in bioimaging. Effective bioimaging requires fluorophores with diverse colors and high quantum yields for better resolution. An essential computational component to design novel dye molecules is an accurate model that predicts the electronic properties of molecules. Here, we present statistical machines that ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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PySHS: Python Open Source Software for Second Harmonic Scattering.

Lotfi Boudjema, Hanna Aarrass, Marwa Assaf, Marie Morille, Gaelle Martin-Gassin, Pierre-Marie Gassin,

The PySHS package is a new python open source software tool which simulates the second harmonic scattering (SHS) of different kinds of colloidal nano-objects in various experimental configurations. This package is able to compute polarizations resolved at a fixed scattered angle or angular distribution for different polarization configurations. This article ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Topological Similarity Search in Large Combinatorial Fragment Spaces.

Louis Bellmann, Patrick Penner, Matthias Rarey,

In similarity-driven virtual screening, molecular fingerprints are widely used to assess the similarity of all compounds contained in a chemical library to a query compound of interest. This similarity analysis is traditionally done for each member of the library individually. When encoding chemical spaces that surpass billions of compounds in ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies.

Michael L Drummond, Andrew Henry, Huifang Li, Christopher I Williams,

Extending upon our previous publication [Drummond, M.; J. Chem. Inf. Model. 2019, 59, 1634-1644], two additional computational methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Ensemble-Based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small-Molecule Ligands.

Bin Chong, Yingguang Yang, Chenguang Zhou, Qiaojing Huang, Zhirong Liu,

In contrast to the "lock-and-key" model underlying the long-term success of structural biology and rational drug design, intrinsically disordered proteins (IDPs) exist in an ensemble of highly heterogeneous conformations even after binding with small-molecule ligands. It remains controversial how to characterize the thermodynamics of such fuzzy interactions. Here, we derive ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints.

David J Ponting, Ruud van Deursen, Martin A Ott,

Prediction of whether a compound is "aromatic" is at first glance a relatively simple task-does it obey Hückel's rule (planar cyclic π-system with 4n + 2 electrons) or not? However, aromaticity is far from a binary property, and there are distinct variations in the chemical and biological behavior of different ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Comparing Fingerprints for Ligand-Based Virtual Screening: A Fast and Scalable Approach for Unbiased Evaluation.

Lewis J Martin, Michael T Bowen,

Ligand-based virtual screening is a useful tool for drug and probe discovery due to its high accessibility and scalability. The recent identification of bias in many data sets that were used in performance evaluation, quantified by the asymmetric validation embedding (AVE) score, has prompted the reanalysis of models to determine ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks.

Alex D Casey, Steven F Son, Ilias Bilionis, Brian C Barnes,

We develop a convolutional neural network capable of directly parsing the 3D electronic structure of a molecule described by spatial point data for charge density and electrostatic potential represented as a 4D tensor. This method effectively bypasses the need to construct complex representations, or descriptors, of a molecule. This is ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Mechanism of Dynamic Binding of Replication Protein A to ssDNA.

Anupam Mondal, Arnab Bhattacherjee,

Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with single-stranded DNA (ssDNA) intermediates before handing them over to downstream proteins. The length of ssDNA ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization.

James A Lumley, Prashant Desai, Jibo Wang, Suntara Cahya, Hongzhou Zhang,

Matched Molecular Pairs (MMP) analysis is a well-established technique for Structure Activity and Property Analysis (SAR and SPR). Summarizing multiple MMPs that describe the same structural change into a single chemical transform can be a powerful tool for prediction (termed Transform from here on). This is particularly useful in the ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Bayesian Algorithm for Retrosynthesis.

Zhongliang Guo, Stephen Wu, Mitsuru Ohno, Ryo Yoshida,

The identification of synthetic routes that end with the desired product is considered an inherently time-consuming process that is largely dependent on expert knowledge regarding a limited proportion of the entire reaction space. At present, emerging machine learning technologies are reformulating the process of retrosynthetic planning. This study aimed to ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space.

Nivedita Dutta, Joanna Sarzynska, Ansuman Lahiri,

There are only four derivatives of pseudouridine (Ψ) that are known to occur naturally in RNA as post-transcriptional modifications. We have studied the conformational consequences of pseudouridylation and further modifications using replica exchange molecular dynamics simulations at the nucleoside level, and the simulated conformational preferences were compared with the available ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Dissecting the Molecular Mechanism of Colistin Resistance in mcr-1 Bacteria.

Jianguo Li, Roger Beuerman, Chandra S Verma,

Colistin or polymyxin B is the last resort antibiotic to treat infections of multidrug-resistant Gram-negative bacteria by disrupting their outer membranes. The recent emergence of Gram-negative bacteria that demonstrate colistin resistance, particularly plasmid-mediated mobile colistin resistance (mcr), poses a big challenge to the treatment of multidrug resistance infections. Using molecular ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Discovery of a New Donepezil-like Acetylcholinesterase Inhibitor for Targeting Alzheimer's Disease: Computational Studies with Biological Validation.

Bashir Akhlaq Akhoon, Sushil Choudhary, Harshita Tiwari, Ajay Kumar, Manas Ranjan Barik, Laxmi Rathor, Rakesh Pandey, Amit Nargotra,

Alzheimer's disorder is one of the most common worldwide health problems, and its prevalence continues to increase, thereby straining the healthcare budgets of both developed and developing countries. So far, donepezil is the only Food and Drug Administration-approved dual-binding site inhibitor of acetylcholinesterase (AChE) that can amplify the cholinergic activity ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery.

Jacques Boitreaud, Vincent Mallet, Carlos Oliver, Jérôme Waldispühl,

Ligand-based drug design has recently benefited from the development of deep generative models. These models enable extensive explorations of the chemical space and provide a platform for molecular optimization. However, the vast majority of current methods does not leverage the structure of the binding target, which potentiates the binding of ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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PI1M: A Benchmark Database for Polymer Informatics.

Ruimin Ma, Tengfei Luo,

Open-source data on large scale are the cornerstones for data-driven research, but they are not readily available for polymers. In this work, we build a benchmark database, called PI1M (referring to ∼1 million polymers for polymer informatics), to provide data resources that can be used for machine learning research in ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex.

Holli-Joi Sullivan, Brian Chen, Chun Wu,

DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.

Lindsey Burggraaff, Amber van Veen, Chi Chung Lam, Herman W T van Vlijmen, Adriaan P IJzerman, Gerard J P van Westen,

Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to a protein noncompetitively with ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

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