4.7 Article

Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices

Related references

Note: Only part of the references are listed.
Article Chemistry, Medicinal

Diversity and Chemical Library Networks of Large Data Sets

Timothy B. Dunn et al.

Summary: The quantification of chemical diversity has extensive applications across various fields. With the expansion of chemical libraries, it is crucial to develop efficient methods for quantifying and visualizing the diversity of large-scale chemical libraries. This article introduces a new extended similarity indices method to measure the fingerprint-based diversity of chemical libraries and proposes the Chemical Library Networks (CLNs) framework for visually representing the chemical space of large libraries.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

Article Chemistry, Medicinal

Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets

E. Alexis Flores-Padilla et al.

Summary: The importance of epigenetic drug and probe discovery is increasing, aiding in the development of therapeutic treatments and understanding underlying epigenetic mechanisms in biological processes. Through comprehensive analysis of eleven libraries focused on epigenetic targets, guidance is provided for experimental groups working with high-throughput and medium-throughput screening of epigenetic-focused libraries, and as a reference for designing novel focused epigenetic libraries.

MOLECULAR INFORMATICS (2022)

Article Biochemistry & Molecular Biology

Extended continuous similarity indices: theory and application for QSAR descriptor selection

Anita Racz et al.

Summary: Extended similarity indices improve the efficiency of binary string comparison and have applications in various fields. However, the current indices are limited to binary or categorical inputs. We propose a further generalization to apply the indices to numerical data with continuous components and discuss different implementation methods and their analytical properties.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2022)

Article Chemistry, Physical

Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors

Wesley B. Cardoso et al.

Summary: The study revealed that despite molecular differences, HIV protease inhibitors showed similar behavior in combating SARS-CoV-2 at the molecular level.

JOURNAL OF MOLECULAR STRUCTURE (2021)

Article Chemistry, Physical

Improving the analysis of biological ensembles through extended similarity measures

Liwei Chang et al.

Summary: The paper introduces new algorithms for classifying structural ensembles of macromolecules using extended similarity measures which reduce computational complexity. The approach captures larger ensembles and transitions between states, developing efficient techniques and a novel clustering algorithm utilizing the extended similarity indices. The new metrics are applied to analyze biological systems' ensembles, showing excellent performance and faster processing, with an efficient cost-function for merging clusters.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2021)

Article Multidisciplinary Sciences

An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19

Dafydd R. Owen et al.

Summary: PF-07321332, an orally bioavailable SARS-CoV-2 main protease inhibitor, has been discovered with in vitro pan-human coronavirus antiviral activity and excellent off-target selectivity and in vivo safety profiles. This new drug has shown promise in countering the threat of COVID-19 with its oral activity and safety in clinical trials.

SCIENCE (2021)

Article Chemistry, Medicinal

Differential Consistency Analysis: Which Similarity Measures can be Applied in Drug Discovery?

Ramon Alain Miranda-Quintana et al.

Summary: The study investigates the conditions under which two comparative measures provide equivalent results on a given set of molecules. A novel method (Differential Consistency Analysis) is introduced to study the consistency between comparative measures, revealing that using a reference with less variation in similarity or representing molecules in a size-independent way can improve consistency. The presented derivations are applicable to all binary similarity coefficients introduced so far, regardless of molecular representations.

MOLECULAR INFORMATICS (2021)

Article Chemistry, Multidisciplinary

Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection

Ramon Alain Miranda-Quintana et al.

Summary: The study introduces a new method for multi-molecular similarity calculations, allowing comparisons of more than two molecules at a time and defining a series of novel indices. These indices demonstrate high speed and accuracy in practical applications, providing better results in selecting compound sets or measuring dataset compactness.

JOURNAL OF CHEMINFORMATICS (2021)

Article Chemistry, Multidisciplinary

Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 1: Theory and characteristics

Ramon Alain Miranda-Quintana et al.

Summary: This study introduces a straightforward computational framework for comparing multiple objects at the same time and provides extended formulas for a wide selection of similarity metrics. The analysis on the effects of various parameters on the similarity values calculated by the extended formulas is detailed. Two types of variance analysis help to understand the main features of the extended similarity indices.

JOURNAL OF CHEMINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Machine learning models for classification tasks related to drug safety

Anita Racz et al.

Summary: This review outlines current trends in machine learning-driven classification studies related to ADME and toxicity endpoints from the past six years, focusing on large datasets and comparing different endpoints. The dominance of tree-based algorithms and the increasing trend of consensus modeling for drug safety predictions were identified as key findings from the evaluation of the data.

MOLECULAR DIVERSITY (2021)

Article Biochemistry & Molecular Biology

Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors

Levente M. Mihalovits et al.

Summary: The ubiquitin-proteasome system plays a critical role in protein degradation and key cellular processes. The immunoproteasome is induced during disease processes and inhibiting it can be beneficial in treating cancer, autoimmune disorders, and neurodegenerative diseases. Further research is needed to understand the mechanism of oxathiazolones in selectively inhibiting the immunoproteasome over the constitutive proteasome.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Extended many-item similarity indices for sets of nucleotide and protein sequences

David Bajusz et al.

Summary: The text discusses a method for calculating similarities between multiple sequences, introducing new symmetric similarity indices and analyzing them in detail with variance analysis, demonstrated with three protein/DNA sequence case studies. This approach allows for a more accurate quantification of similarities between different sequences.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Chemistry, Multidisciplinary

Classical molecular dynamics on graphics processing unit architectures

Adam Jasz et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

Article Biochemistry & Molecular Biology

Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling

Anita Racz et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)

Article Multidisciplinary Sciences

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

Alice Douangamath et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations

Levente M. Mihalovits et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

A. Acharya et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Multidisciplinary

On the impossibility of unambiguously selecting the best model for fitting data

Ramon Alain Miranda-Quintana et al.

JOURNAL OF MATHEMATICAL CHEMISTRY (2019)

Article Biochemistry & Molecular Biology

Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock

Ilke Ugur et al.

JOURNAL OF MOLECULAR MODELING (2019)

Article Multidisciplinary Sciences

Structural and functional consequences of the STAT5BN642H driver mutation

Elvin D. de Araujo et al.

NATURE COMMUNICATIONS (2019)

Review Biochemistry & Molecular Biology

Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins

Hao Geng et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2019)

Review Oncology

Structural Implications of STAT3 and STAT5 SH2 Domain Mutations

Elvin D. de Araujo et al.

CANCERS (2019)

Review Biochemistry & Molecular Biology

Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier

Laura Orellana

FRONTIERS IN MOLECULAR BIOSCIENCES (2019)

Article Engineering, Multidisciplinary

Nano-engineering of construction materials using molecular dynamics simulations: Prospects and challenges

Denvid Lau et al.

COMPOSITES PART B-ENGINEERING (2018)

Article Oncology

Pharmacologic inhibition of STAT5 in acute myeloid leukemia

Bettina Wingelhofer et al.

LEUKEMIA (2018)

Review Neurosciences

Molecular Dynamics Simulation for All

Scott A. Hollingsworth et al.

NEURON (2018)

Review Multidisciplinary Sciences

Biophysical experiments and biomolecular simulations: A perfect match?

Sandro Bottaro et al.

SCIENCE (2018)

Article Chemistry, Physical

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Edward Harder et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Medicinal

Role of Molecular Dynamics and Related Methods in Drug Discovery

Marco De Vivo et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Biochemistry & Molecular Biology

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

G. Madhavi Sastry et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Goetz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Multidisciplinary Sciences

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

Giovanni Bottegoni et al.

PLOS ONE (2011)

Article Chemistry, Multidisciplinary

Formal theory of the comparative relations: its application to the study of quantum similarity and dissimilarity measures and indices

Ramon-Alain Miranda-Quintana et al.

JOURNAL OF MATHEMATICAL CHEMISTRY (2010)

Review Biochemistry & Molecular Biology

Flexible ligand docking to multiple receptor conformations: a practical alternative

Maxim Totrov et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)

Article Multidisciplinary Sciences

Clustering by passing messages between data points

Brendan J. Frey et al.

SCIENCE (2007)

Review Biotechnology & Applied Microbiology

Predicting in vivo drug interactions from in vitro drug discovery data

LC Wienkers et al.

NATURE REVIEWS DRUG DISCOVERY (2005)