From Brazil to Germany: Challenges and Advantages.

Abstract:

:Moving to a new country, with a different culture and a new environment, is not an easy decision. In this perspective, I present some reasons that made me, a Brazilian computational biochemist, move abroad to do postdoctoral research and some of the challenges I faced before and after moving.

journal_name

J Chem Inf Model

authors

Nunes-Alves A

doi

10.1021/acs.jcim.9b00764

subject

Has Abstract

pub_date

2020-02-24 00:00:00

pages

449-451

issue

2

eissn

1549-9596

issn

1549-960X

journal_volume

60

pub_type

杂志文章
  • New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism.

    abstract::Cytochrome P450 3A4 metabolizes nearly 50% of the drugs currently in clinical use with a broad range of substrate specificity. Early prediction of metabolites of xenobiotic compounds is crucial for cost efficient drug discovery and development. We developed a new combined model, MLite, for the prediction of regioselec...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci7003576

    authors: Oh WS,Kim DN,Jung J,Cho KH,No KT

    更新日期:2008-03-01 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

  • Searching for coordinated activity cliffs using particle swarm optimization.

    abstract::Activity cliffs are formed by structurally similar compounds having large potency differences. Coordinated activity cliffs evolve when compounds within groups of structural neighbors form multiple cliffs with different partners, giving rise to local networks of cliffs in a data set. Using particle swarm optimization, ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3000503

    authors: Namasivayam V,Bajorath J

    更新日期:2012-04-23 00:00:00

  • Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase.

    abstract::The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes t...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00675

    authors: Cossio-Pérez R,Pierdominici-Sottile G,Sobrado P,Palma J

    更新日期:2019-02-25 00:00:00

  • Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid.

    abstract::Designing organic saccharide sensors for use in aqueous solution is a nontrivial endeavor. Incorporation of hydrogen bonding groups on a sensor's receptor unit to target saccharides is an obvious strategy but not one that is likely to ensure analyte-receptor interactions over analyte-solvent or receptor-solvent intera...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00987

    authors: Kearns FL,Robart C,Kemp MT,Vankayala SL,Chapin BM,Anslyn EV,Woodcock HL,Larkin JD

    更新日期:2019-05-28 00:00:00

  • BFMP: a method for discretizing and visualizing pyranose conformations.

    abstract::We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automate...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500325b

    authors: Makeneni S,Foley BL,Woods RJ

    更新日期:2014-10-27 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

  • Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

    abstract::Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00235

    authors: Zhang Q,Xu Z,Shi J,Zhu W

    更新日期:2017-07-24 00:00:00

  • Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries.

    abstract::The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200078f

    authors: Li L,Wang B,Meroueh SO

    更新日期:2011-09-26 00:00:00

  • Automated pharmacophore query optimization with genetic algorithms - a case study using the MC4R system.

    abstract::Due to the recent availability of high quality small molecule databases, such as ZINC and PubChem,1,2 virtual screening is playing an even more important role in identifying biologically relevant molecules in drug discovery campaigns. The success of pharmacophore-based virtual screening (PBVS) relies largely on the ac...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700089w

    authors: Jia L,Zou J,So SS,Sun H

    更新日期:2007-07-01 00:00:00

  • Database of Nuclear Independent Chemical Shifts (NICS) versus NICSZZ of Polycyclic Aromatic Hydrocarbons (PAHs).

    abstract::In the present contribution, we have developed a database, called the FAR-database, where the acronym FAR stands for Fused Aromatic Rings, which presents the results of nuclear independent chemical shifts calculations, NICS(0), NICS(1), NICS(0)ZZ, and NICS(1)ZZ, of 660 neutral benzenoid-PAHs and cyclopenta-fused PAHs....

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00909

    authors: Alvarez-Ramírez F,Ruiz-Morales Y

    更新日期:2020-02-24 00:00:00

  • Rapid evaluation of synthetic and molecular complexity for in silico chemistry.

    abstract::Methods that rapidly evaluate molecular complexity and synthetic feasibility are becoming increasingly important for in silico chemistry. We propose a new metric based on relative atomic electronegativities and bond parameters that evaluate both synthetic and molecular complexity (SMCM) starting from chemical structur...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0501387

    authors: Allu TK,Oprea TI

    更新日期:2005-09-01 00:00:00

  • Role of halogen bonds in thyroid hormone receptor selectivity: pharmacophore-based 3D-QSSR studies.

    abstract::Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TRalpha and TRbeta. Several pharmacological effects mediated by TRbeta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TRbeta activation may el...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900316e

    authors: Valadares NF,Salum LB,Polikarpov I,Andricopulo AD,Garratt RC

    更新日期:2009-11-01 00:00:00

  • Characterization of Hydration Properties in Structural Ensembles of Biomolecules.

    abstract::Solute-solvent interactions are critical for biomolecular stability and recognition. Explicit solvent molecular dynamics (MD) simulations are routinely used to probe such interactions. However, detailed analyses and interpretation of the hydration patterns seen in MD simulations can be both complex and time-consuming....

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00453

    authors: Pradhan MR,Nguyen MN,Kannan S,Fox SJ,Kwoh CK,Lane DP,Verma CS

    更新日期:2019-07-22 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

  • Spatial sign preprocessing: a simple way to impart moderate robustness to multivariate estimators.

    abstract::The spatial sign is a multivariate extension of the concept of sign. Recently multivariate estimators of covariance structures based on spatial signs have been examined by various authors. These new estimators are found to be robust to outlying observations. From a computational point of view, estimators based on spat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050498u

    authors: Serneels S,De Nolf E,Van Espen PJ

    更新日期:2006-05-01 00:00:00

  • Ranking chemical structures for drug discovery: a new machine learning approach.

    abstract::With chemical libraries increasingly containing millions of compounds or more, there is a fast-growing need for computational methods that can rank or prioritize compounds for screening. Machine learning methods have shown considerable promise for this task; indeed, classification methods such as support vector machin...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci9003865

    authors: Agarwal S,Dugar D,Sengupta S

    更新日期:2010-05-24 00:00:00

  • Ligand coordinate analysis of SC-558 from the active site to the surface of COX-2: a molecular dynamics study.

    abstract::We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published cryst...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050142i

    authors: Sai Ram KV,Rambabu G,Sarma JA,Desiraju GR

    更新日期:2006-07-01 00:00:00

  • Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions.

    abstract::Taking into account dynamical behavior and/or structural inaccuracies of receptor-ligand systems becomes increasingly important in structure-based drug design. Here, we describe the development of consensus Adaptation of Fields for Molecular Comparison (AFMoC) (abbreviated as AFMoCcon) models that account for multiple...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci7002472

    authors: Breu B,Silber K,Gohlke H

    更新日期:2007-11-01 00:00:00

  • 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

  • Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

    abstract::We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assemb...

    journal_title:Journal of chemical information and modeling

    pub_type: 信件

    doi:10.1021/acs.jcim.8b00193

    authors: Kang M,Chakraborty K,Loverde SM

    更新日期:2018-06-25 00:00:00

  • RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application.

    abstract::There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here we introduce RDChiral, an open-source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying ret...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00286

    authors: Coley CW,Green WH,Jensen KF

    更新日期:2019-06-24 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

  • TAMkin: a versatile package for vibrational analysis and chemical kinetics.

    abstract::TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100099g

    authors: Ghysels A,Verstraelen T,Hemelsoet K,Waroquier M,Van Speybroeck V

    更新日期:2010-09-27 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

  • Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA.

    abstract::The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called "ω-loop", so that the substrates can enter the active site. He...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00211

    authors: Duclert-Savatier N,Bouvier G,Nilges M,Malliavin TE

    更新日期:2016-09-26 00:00:00

  • On three-electron bonds and hydrogen bonds in the open-shell complexes [H2X2]+ for X = F, Cl, and Br.

    abstract::The [H2X2]+ (X = Cl, Br) formula could refer to two possible stable structures, namely, the hydrogen-bonded complex and the three-electron-bonded one. In contrary to the results published by other authors, we claim that for the F-type structures the hydrogen-bonded form is the only possible one and the [HFFH]+ complex...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600355g

    authors: Bil A,Berski S,Latajka Z

    更新日期:2007-05-01 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

  • Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity.

    abstract::Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissu...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci8002182

    authors: Salum LB,Polikarpov I,Andricopulo AD

    更新日期:2008-11-01 00:00:00

  • Universal Activation Index for Class A GPCRs.

    abstract::An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00604

    authors: Ibrahim P,Wifling D,Clark T

    更新日期:2019-09-23 00:00:00