Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design.

Abstract:

:The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, derived from protein-ligand complexes, consisting of complexes of ligands with protein fragments (such as amino-acid side chains), with interaction energies based on MP2-F12 and DLPNO-CCSD(T) calculations. From these, composite benchmark interaction energies are also built for complexes of the ligand with the complete active site of the protein (PLA15 data set). These data sets are used to test multiple SQM methods with corrections for noncovalent interactions; the role of the solvation model in the calculations is tested as well.

journal_name

J Chem Inf Model

authors

Kříž K,Řezáč J

doi

10.1021/acs.jcim.9b01171

subject

Has Abstract

pub_date

2020-03-23 00:00:00

pages

1453-1460

issue

3

eissn

1549-9596

issn

1549-960X

journal_volume

60

pub_type

杂志文章
  • PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS.

    abstract::We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00305

    authors: Istyastono EP,Radifar M,Yuniarti N,Prasasty VD,Mungkasi S

    更新日期:2020-08-24 00:00:00

  • Combinatorial × computational × cheminformatics (C3) approach to characterization of congeneric libraries of organic pollutants.

    abstract::Congeners are molecules based on the same carbon skeleton but are different by the number of substituents and/or a substitution pattern. Examples are 1-chloronaphthalene, 1,4-dichloronaphthalene, and 1,3,8-trichloronaphthalene. Various persistent organic pollutants (POPs) exist in the environment as families of congen...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300289b

    authors: Haranczyk M,Urbaszek P,Ng EG,Puzyn T

    更新日期:2012-11-26 00:00:00

  • Interpretation of the binding affinities of PTP1B inhibitors with the MM-GB/SA method and the X-score scoring function.

    abstract::We have studied the binding affinities of a set of 45 small-molecule inhibitors to protein tyrosine phosphatase 1B (PTP1B) through computational approaches. All of these compounds share a common oxalylamino benzoic acid (OBA) moiety. The complex structure of each compound was modeled by using the GOLD program plus the...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci8004429

    authors: Zhang X,Li X,Wang R

    更新日期:2009-04-01 00:00:00

  • Gas-phase and solution conformations of selected dimeric structural units of heparin.

    abstract::The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is sta...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci060060+

    authors: Remko M,von der Lieth CW

    更新日期:2006-07-01 00:00:00

  • Conformational analysis of macrocycles: finding what common search methods miss.

    abstract::As computational drug design becomes increasingly reliant on virtual screening and on high-throughput 3D modeling, the need for fast, robust, and reliable methods for sampling molecular conformations has become greater than ever. Furthermore, chemical novelty is at a premium, forcing medicinal chemists to explore more...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900238a

    authors: Bonnet P,Agrafiotis DK,Zhu F,Martin E

    更新日期:2009-10-01 00:00:00

  • Truncated variants of the GCN4 transcription activator protein bind DNA with dramatically different dynamical motifs.

    abstract::The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of alpha helices formed at the DNA-binding interface. While experiments have shown that truncated versions of the protein retain biologically relevant DNA-bind...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500448e

    authors: McHarris DM,Barr DA

    更新日期:2014-10-27 00:00:00

  • In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window.

    abstract::In this study, two probabilistic machine-learning algorithms were compared for in silico target prediction of bioactive molecules, namely the well-established Laplacian-modified Naïve Bayes classifier (NB) and the more recently introduced (to Cheminformatics) Parzen-Rosenblatt Window. Both classifiers were trained in ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300435j

    authors: Koutsoukas A,Lowe R,Kalantarmotamedi Y,Mussa HY,Klaffke W,Mitchell JB,Glen RC,Bender A

    更新日期:2013-08-26 00:00:00

  • Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening, and experimental validation.

    abstract::Inhibitors of histone deacetylases (HDACIs) have emerged as a new class of drugs for the treatment of human cancers and other diseases because of their effects on cell growth, differentiation, and apoptosis. In this study we have developed several quantitative structure-activity relationship (QSAR) models for 59 chemi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800366f

    authors: Tang H,Wang XS,Huang XP,Roth BL,Butler KV,Kozikowski AP,Jung M,Tropsha A

    更新日期:2009-02-01 00:00:00

  • An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors.

    abstract::A novel approach was developed to rationally interface structure- and ligand-based drug design through the rescoring of docking poses and automated generation of molecular alignments for 3D quantitative structure-activity relationship investigations. The procedure was driven by a genetic algorithm optimizing the value...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800015s

    authors: Nicolotti O,Miscioscia TF,Carotti A,Leonetti F,Carotti A

    更新日期:2008-06-01 00:00:00

  • Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets.

    abstract::With the emergence of large collections of protein-ligand complexes complemented by binding data, as found in PDBbind or BindingMOAD, new opportunities for parametrizing and evaluating scoring functions have arisen. With huge data collections available, it becomes feasible to fit scoring functions in a QSAR style, i.e...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100264e

    authors: Kramer C,Gedeck P

    更新日期:2010-11-22 00:00:00

  • Improved Chemical Structure-Activity Modeling Through Data Augmentation.

    abstract::Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spect...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00570

    authors: Cortes-Ciriano I,Bender A

    更新日期:2015-12-28 00:00:00

  • Study of Data Set Modelability: Modelability, Rivality, and Weighted Modelability Indexes.

    abstract::The knowledge of the capacity of a data set to be modeled in the first stages of the building of quantitative structure-activity relationship (QSAR) prediction models is an important issue because it might reduce the effort and time necessary to select or reject data sets and in refining the data set's composition. Th...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00188

    authors: Luque Ruiz I,Gómez-Nieto MÁ

    更新日期:2018-09-24 00:00:00

  • Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

    abstract::The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00001

    authors: Wang M,Li P,Jia X,Liu W,Shao Y,Hu W,Zheng J,Brooks BR,Mei Y

    更新日期:2017-10-23 00:00:00

  • Flux (1): a virtual synthesis scheme for fragment-based de novo design.

    abstract::It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builde...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503560

    authors: Fechner U,Schneider G

    更新日期:2006-03-01 00:00:00

  • Mesoscopic simulation of phospholipid membranes, peptides, and proteins with molecular fragment dynamics.

    abstract::Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connecte...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci5006096

    authors: Truszkowski A,van den Broek K,Kuhn H,Zielesny A,Epple M

    更新日期:2015-05-26 00:00:00

  • In vitro drug sensitivity-gene expression correlations involve a tissue of origin dependency.

    abstract::A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci060073n

    authors: Andersson CR,Fryknäs M,Rickardson L,Larsson R,Isaksson A,Gustafsson MG

    更新日期:2007-01-01 00:00:00

  • DiSCuS: an open platform for (not only) virtual screening results management.

    abstract::DiSCuS, a "Database System for Compound Selection", has been developed. The primary goal of DiSCuS is to aid researchers in the steps subsequent to generating high-throughput virtual screening (HTVS) results, such as selection of compounds for further study, purchase, or synthesis. To do so, DiSCuS provides (1) a stor...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400587f

    authors: Wójcikowski M,Zielenkiewicz P,Siedlecki P

    更新日期:2014-01-27 00:00:00

  • Residue preference mapping of ligand fragments in the Protein Data Bank.

    abstract::The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables u...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100386y

    authors: Wang L,Xie Z,Wipf P,Xie XQ

    更新日期:2011-04-25 00:00:00

  • Radial clustergrams: visualizing the aggregate properties of hierarchical clusters.

    abstract::A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600427x

    authors: Agrafiotis DK,Bandyopadhyay D,Farnum M

    更新日期:2007-01-01 00:00:00

  • Three-dimensional quantitative structure-activity relationship of nucleosides acting at the A3 adenosine receptor: analysis of binding and relative efficacy.

    abstract::The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600501z

    authors: Kimand SK,Jacobson KA

    更新日期:2007-05-01 00:00:00

  • Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα.

    abstract::Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00202

    authors: Bergant Loboda K,Janežič M,Štampar M,Žegura B,Filipič M,Perdih A

    更新日期:2020-07-27 00:00:00

  • Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches.

    abstract::Protein dynamics play a critical role in ligand binding, and different models have been proposed to explain the relationships between protein motion and molecular recognition. Here, we present a study of ligand-binding processes associated with large conformational changes of a protein to elucidate the critical choice...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00125

    authors: Motta S,Bonati L

    更新日期:2017-07-24 00:00:00

  • Homology modeling and docking evaluation of aminergic G protein-coupled receptors.

    abstract::We report the development of homology models of dopamine (D(2), D(3), and D(4)), serotonin (5-HT(1B), 5-HT(2A), 5-HT(2B), and 5-HT(2C)), histamine (H(1)), and muscarinic (M(1)) receptors, based on the high-resolution structure of the beta(2)-adrenergic receptor. The homology models were built and refined using Prime. ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900444q

    authors: McRobb FM,Capuano B,Crosby IT,Chalmers DK,Yuriev E

    更新日期:2010-04-26 00:00:00

  • Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors.

    abstract::One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00847

    authors: da Costa CHS,Bonatto V,Dos Santos AM,Lameira J,Leitão A,Montanari CA

    更新日期:2020-02-24 00:00:00

  • Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization.

    abstract::Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00063

    authors: Xu L,Shan S,Chen Y,Wang X,Nussinov R,Ma B

    更新日期:2015-06-22 00:00:00

  • Ligand binding determinants for angiotensin II type 1 receptor from computer simulations.

    abstract::The ligand binding determinants for the angiotensin II type 1 receptor (AT1R), a G protein-coupled receptor (GPCR), have been characterized by means of computer simulations. As a first step, a pharmacophore model of various known AT1R ligands exhibiting a wide range of binding affinities was generated. Second, a struc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400400m

    authors: Matsoukas MT,Cordomí A,Ríos S,Pardo L,Tselios T

    更新日期:2013-11-25 00:00:00

  • Combined Experimental and Molecular Simulation Study of Insulin-Chitosan Complexation Driven by Electrostatic Interactions.

    abstract::Protein-polysaccharide complexes constructed via self-assembly methods are often used to develop novel biomaterials for a wide range of applications in biomedicine, food, and biotechnology. The objective of this work was to investigate theoretically and to demonstrate via constant-pH Monte Carlo simulations that the c...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00814

    authors: Prudkin-Silva C,Pérez OE,Martínez KD,Barroso da Silva FL

    更新日期:2020-02-24 00:00:00

  • ANN multiscale model of anti-HIV drugs activity vs AIDS prevalence in the US at county level based on information indices of molecular graphs and social networks.

    abstract::This work is aimed at describing the workflow for a methodology that combines chemoinformatics and pharmacoepidemiology methods and at reporting the first predictive model developed with this methodology. The new model is able to predict complex networks of AIDS prevalence in the US counties, taking into consideration...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400716y

    authors: González-Díaz H,Herrera-Ibatá DM,Duardo-Sánchez A,Munteanu CR,Orbegozo-Medina RA,Pazos A

    更新日期:2014-03-24 00:00:00

  • RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks.

    abstract::The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development, represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key ste...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00075

    authors: Hassan-Harrirou H,Zhang C,Lemmin T

    更新日期:2020-06-22 00:00:00

  • Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study.

    abstract::Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate-dependent enzyme involved in the biosynthesis of valine, leucine, isoleucine, and lysine. Experimental evidence has shown that mutation of the Gln202 residue results in a decrease in the enzymatic activity, thus suggesting the main role of the carboligation cat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00863

    authors: Mendoza F,Medina FE,Jiménez VA,Jaña GA

    更新日期:2020-02-24 00:00:00