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 HIPPOS speeds up the computational times by separating the reference generation and docking analysis. PyPLIF HIPPOS also offers more options compared to PyPLIF. PyPLIF HIPPOS for Linux is stored as the Supporting Information in this application note and can be accessed in GitHub (https://github.com/radifar/PyPLIF-HIPPOS). Additionally, we present here the application of the tool in a retrospective structure-based virtual screening campaign targeting neuraminidase.

journal_name

J Chem Inf Model

authors

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

doi

10.1021/acs.jcim.0c00305

subject

Has Abstract

pub_date

2020-08-24 00:00:00

pages

3697-3702

issue

8

eissn

1549-9596

issn

1549-960X

journal_volume

60

pub_type

杂志文章
  • 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

  • Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software.

    abstract::Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of (1)H and (13)C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated (1)H and (1...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00083

    authors: Kapaev RR,Toukach PV

    更新日期:2016-06-27 00:00:00

  • Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations.

    abstract::Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most wid...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01168

    authors: Rusu VH,Santos DES,Poleto MD,Galheigo MM,Gomes ATA,Verli H,Soares TA,Lins RD

    更新日期:2020-12-28 00:00:00

  • Reaction site mapping of xenobiotic biotransformations.

    abstract::Predictive metabolism methods can be used in drug discovery projects to enhance the understanding of structure-metabolism relationships. The present study uses data mining methods to exploit biotransformation data that have been recorded in the MDL Metabolite database. Reacting center fingerprints were derived from a ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600376q

    authors: Boyer S,Arnby CH,Carlsson L,Smith J,Stein V,Glen RC

    更新日期:2007-03-01 00:00:00

  • Target-independent prediction of drug synergies using only drug lipophilicity.

    abstract::Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descr...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500276x

    authors: Yilancioglu K,Weinstein ZB,Meydan C,Akhmetov A,Toprak I,Durmaz A,Iossifov I,Kazan H,Roth FP,Cokol M

    更新日期:2014-08-25 00:00:00

  • Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models.

    abstract::Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are th...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01178

    authors: Gong W,Liu Y,Zhao Y,Wang S,Han Z,Li C

    更新日期:2021-01-26 00:00:00

  • Efficient calculation of molecular properties from simulation using kernel molecular dynamics.

    abstract::Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many pro...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci8001233

    authors: Brown WM,Sasson A,Bellew DR,Hunsaker LA,Martin S,Leitao A,Deck LM,Vander Jagt DL,Oprea TI

    更新日期:2008-08-01 00:00:00

  • PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data.

    abstract::Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. The PythoMS framewor...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00055

    authors: Yunker LPE,Donnecke S,Ting M,Yeung D,McIndoe JS

    更新日期:2019-04-22 00:00:00

  • The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant.

    abstract::We have performed a systematic study of the entropy term in the MM/GBSA (molecular mechanics combined with generalized Born and surface-area solvation) approach to calculate ligand-binding affinities. The entropies are calculated by a normal-mode analysis of harmonic frequencies from minimized snapshots of molecular d...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3001919

    authors: Genheden S,Kuhn O,Mikulskis P,Hoffmann D,Ryde U

    更新日期:2012-08-27 00:00:00

  • In silico prediction of aqueous solubility: the solubility challenge.

    abstract::The dissolution of a chemical into water is a process fundamental to both chemistry and biology. The persistence of a chemical within the environment and the effects of a chemical within the body are dependent primarily upon aqueous solubility. With the well-documented limitations hindering the accurate experimental d...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900286s

    authors: Hewitt M,Cronin MT,Enoch SJ,Madden JC,Roberts DW,Dearden JC

    更新日期:2009-11-01 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

  • Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

    abstract::On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00143

    authors: Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

    更新日期:2015-06-22 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

  • Identification of ligand templates using local structure alignment for structure-based drug design.

    abstract::With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300178e

    authors: Lee HS,Im W

    更新日期:2012-10-22 00:00:00

  • Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators.

    abstract::Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but h...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00624

    authors: Lautala S,Provenzani R,Koivuniemi A,Kulig W,Talman V,Róg T,Tuominen RK,Yli-Kauhaluoma J,Bunker A

    更新日期:2020-11-23 00:00:00

  • CoNTub v2.0--algorithms for constructing C3-symmetric models of three-nanotube junctions.

    abstract::Here, a method is described for easily building three-carbon nanotube junctions. It allows the geometry to be found and bond connectivity of C(3) symmetric nanotube junctions to be established. Such junctions may present a variable degree of pyramidalization and are composed of three identical carbon nanotubes with ar...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200056p

    authors: Melchor S,Martin-Martinez FJ,Dobado JA

    更新日期:2011-06-27 00:00:00

  • FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space.

    abstract::An essential feature of all practical de novo molecule generating programs is the ability to focus the potential combinatorial explosion of grown molecules on a desired chemical space. It is a daunting task to balance the generation of new molecules with limitations on growth that produce desired features such as stab...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci9000458

    authors: Kutchukian PS,Lou D,Shakhnovich EI

    更新日期:2009-07-01 00:00:00

  • A Grid Map Based Approach to Identify Nonobvious Ligand Design Opportunities in 3D Protein Structure Ensembles.

    abstract::Three-dimensional protein structures are a key requisite for structure-based drug discovery. For many highly relevant targets, medicinal chemists are confronted with large numbers of target structures in their apo-forms or in complex with a wealth of different ligands. To exploit the full potential of such structure e...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00051

    authors: Schmalhorst PS,Bergner A

    更新日期:2020-04-27 00:00:00

  • Prediction of synthetic accessibility based on commercially available compound databases.

    abstract::A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500568d

    authors: Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

    更新日期:2014-12-22 00:00:00

  • Including explicit water molecules as part of the protein structure in MM/PBSA calculations.

    abstract::Water is the natural medium of molecules in the cell and plays an important role in protein structure, function and interaction with small molecule ligands. However, the widely used molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method for binding energy calculation does not explicitly take account of wa...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci4001794

    authors: Zhu YL,Beroza P,Artis DR

    更新日期:2014-02-24 00:00:00

  • Antihypertensive drug valsartan in solution and at the AT1 receptor: conformational analysis, dynamic NMR spectroscopy, in silico docking, and molecular dynamics simulations.

    abstract::The conformational properties of AT1 antagonist valsartan have been analyzed both in solution and at the binding site of the receptor. Low energy conformations of valsartan in solution were explored by NMR spectroscopy and molecular modeling studies. The NMR results showed the existence of two distinct and almost isoe...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800427s

    authors: Potamitis C,Zervou M,Katsiaras V,Zoumpoulakis P,Durdagi S,Papadopoulos MG,Hayes JM,Grdadolnik SG,Kyrikou I,Argyropoulos D,Vatougia G,Mavromoustakos T

    更新日期:2009-03-01 00:00:00

  • Predicting Toxicities of Diverse Chemical Pesticides in Multiple Avian Species Using Tree-Based QSAR Approaches for Regulatory Purposes.

    abstract::A comprehensive safety evaluation of chemicals should require toxicity assessment in both the aquatic and terrestrial test species. Due to the application practices and nature of chemical pesticides, the avian toxicity testing is considered as an essential requirement in the risk assessment process. In this study, tre...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00139

    authors: Basant N,Gupta S,Singh KP

    更新日期:2015-07-27 00:00:00

  • Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.

    abstract::In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800420z

    authors: ten Brink T,Exner TE

    更新日期:2009-06-01 00:00:00

  • The assembly-inducing laulimalide/peloruside a binding site on tubulin: molecular modeling and biochemical studies with [³H]peloruside A.

    abstract::We used synthetic peloruside A for the commercial preparation of [³H]peloruside A. The radiolabeled compound bound to preformed tubulin polymer in amounts stoichiometric with the polymer's tubulin content, with an apparent K(d) value of 0.35 μM. A less active peloruside A analogue, (11-R)-peloruside A and laulimalide ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci1002894

    authors: Nguyen TL,Xu X,Gussio R,Ghosh AK,Hamel E

    更新日期:2010-11-22 00:00:00

  • Computational Prediction and Biochemical Analyses of New Inverse Agonists for the CB1 Receptor.

    abstract::Human cannabinoid type 1 (CB1) G-protein coupled receptor is a potential therapeutic target for obesity. The previously predicted and experimentally validated ensemble of ligand-free conformations of CB1 [Scott, C. E. et al. Protein Sci. 2013 , 22 , 101 - 113 ; Ahn, K. H. et al. Proteins 2013 , 81 , 1304 - 1317] are u...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00581

    authors: Scott CE,Ahn KH,Graf ST,Goddard WA 3rd,Kendall DA,Abrol R

    更新日期:2016-01-25 00:00:00

  • Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case.

    abstract::In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifica...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800313h

    authors: Yasuo K,Yamaotsu N,Gouda H,Tsujishita H,Hirono S

    更新日期:2009-04-01 00:00:00

  • Assessing the Protective Activity of a Recently Discovered Phenolic Compound against Oxidative Stress Using Computational Chemistry.

    abstract::The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times an...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00513

    authors: Villuendas-Rey Y,Alvarez-Idaboy JR,Galano A

    更新日期:2015-12-28 00:00:00

  • The valence state combination model: a generic framework for handling tautomers and protonation states.

    abstract::The consistent handling of molecules is probably the most basic and important requirement in the field of cheminformatics. Reliable results can only be obtained if the underlying calculations are independent of the specific way molecules are represented in the input data. However, ensuring consistency is a complex tas...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400724v

    authors: Urbaczek S,Kolodzik A,Rarey M

    更新日期:2014-03-24 00:00:00

  • In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel.

    abstract::The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in sili...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00329

    authors: Zhang Y,Zhang HX,Zheng QC

    更新日期:2020-07-27 00:00:00

  • Relationships between Molecular Complexity, Biological Activity, and Structural Diversity.

    abstract::Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503558

    authors: Schuffenhauer A,Brown N,Selzer P,Ertl P,Jacoby E

    更新日期:2006-03-01 00:00:00