Corrigendum to "Addressing docking pose selection with structure-based deep learning: Recent advances, challenges and opportunities" [Comput Struct Biotechnol J vol. 23 (2024) 2141-2151].

[This corrects the article DOI: 10.1016/j.csbj.2024.05.024.].

Addressing docking pose selection with structure-based deep learning: Recent advances, challenges and opportunities.

Molecular docking is a widely used technique in drug discovery to predict the binding mode of a given ligand to its target. However, the identification of the near-native binding pose in docking experiments still represents a challenging task as the scoring functions currently employed by docking programs are parametrized to predict the binding affinity, and, therefore, they often fail to correctly identify the ligand native binding conformation. Selecting the correct binding mode is crucial to obtaining meaningful results and to conveniently optimizing new hit compounds. Deep learning (DL) algorithms have been an area of a growing interest in this sense for their capability to extract the relevant information directly from the protein-ligand structure. Our review aims to present the recent advances regarding the development of DL-based pose selection approaches, discussing limitations and possible future directions. Moreover, a comparison between the performances of some classical scoring functions and DL-based methods concerning their ability to select the correct binding mode is reported. In this regard, two novel DL-based pose selectors developed by us are presented.

"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases.

The conversion of chemical structures into computer-readable descriptors, able to capture key structural aspects, is of pivotal importance in the field of cheminformatics and computer-aided drug design. Molecular fingerprints represent a widely employed class of descriptors; however, their generation process is time-consuming for large databases and is susceptible to bias. Therefore, descriptors able to accurately detect predefined structural fragments and devoid of lengthy generation procedures would be highly desirable. To meet additional needs, such descriptors should also be interpretable by medicinal chemists, and suitable for indexing databases with trillions of compounds. To this end, we developed-as integral part of EXSCALATE, Dompé's end-to-end drug discovery platform-the DompeKeys (DK), a new substructure-based descriptor set, which encodes the chemical features that characterize compounds of pharmaceutical interest. DK represent an exhaustive collection of curated SMARTS strings, defining chemical features at different levels of complexity, from specific functional groups and structural patterns to simpler pharmacophoric points, corresponding to a network of hierarchically interconnected substructures. Because of their extended and hierarchical structure, DK can be used, with good performance, in different kinds of applications. In particular, we demonstrate how they are very well suited for effective mapping of chemical space, as well as substructure search and virtual screening. Notably, the incorporation of DK yields highly performing machine learning models for the prediction of both compounds' activity and metabolic reaction occurrence. The protocol to generate the DK is freely available at https://dompekeys.exscalate.eu and is fully integrated with the Molecular Anatomy protocol for the generation and analysis of hierarchically interconnected molecular scaffolds and frameworks, thus providing a comprehensive and flexible tool for drug design applications.

Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation.

The ability to determine and predict metabolically labile atom positions in a molecule (also called "sites of metabolism" or "SoMs") is of high interest to the design and optimization of bioactive compounds, such as drugs, agrochemicals, and cosmetics. In recent years, several in silico models for SoM prediction have become available, many of which include a machine-learning component. The bottleneck in advancing these approaches is the coverage of distinct atom environments and rare and complex biotransformation events with high-quality experimental data. Pharmaceutical companies typically have measured metabolism data available for several hundred to several thousand compounds. However, even for metabolism experts, interpreting these data and assigning SoMs are challenging and time-consuming. Therefore, a significant proportion of the potential of the existing metabolism data, particularly in machine learning, remains dormant. Here, we report on the development and validation of an active learning approach that identifies the most informative atoms across molecular data sets for SoM annotation. The active learning approach, built on a highly efficient reimplementation of SoM predictor FAME 3, enables experts to prioritize their SoM experimental measurements and annotation efforts on the most rewarding atom environments. We show that this active learning approach yields competitive SoM predictors while requiring the annotation of only 20% of the atom positions required by FAME 3. The source code of the approach presented in this work is publicly available.

Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative.

Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rarely employed. The present study aims to assess if multiple docking calculations can prove successful in target prediction. In detail, the docking simulations submitted to the MEDIATE initiative are utilized to predict the viral targets involved in the hits retrieved by a recently published cytopathic screening. Multiple docking results are combined by the EFO approach to develop target-specific consensus models. The combination of multiple docking simulations enhances the performances of the developed consensus models (average increases in EF1% value of 40% and 25% when combining three and two docking runs, respectively). These models are able to propose reliable targets for about half of the retrieved hits (31 out of 59). Thus, the study emphasizes that docking simulations might be effective in target identification and provide a convincing validation for the collaborative strategies that inspire the MEDIATE initiative. Disappointingly, cross-target and cross-program correlations suggest that common scoring functions are not specific enough for the simulated target.

Health- and skill-related physical fitness profile of Brazilian children and adolescents: a systematic review / Perfil da aptidão física relacionada à saúde e ao desempenho motor de crianças e adolescentes brasileiros: uma revisão sistemática

Since 1994, the Projeto Esporte Brasil (PROESP-Br) battery tests has been used to evaluate health- and skill-related physical fitness among aged 6-17 Brazilian schoolchildren. The aim of this study was to delineate the Brazilian children and youth's physical fitness profile from a systematic review over studies that used the PROESP-Br proposal. The search was carried at PubMed, ScienceDirect, Lilacs, SciELO and Google Scholar. Original studies published between 1994 and 2017 about physical fitness (health and/or motor performance) with schoolchildren (children and/or adolescents) that used the PROESP-Br battery test were included. A total of 13.582 participants were evaluated to health-related fitness and 276 to skill-related fitness from 18 included studies. The methodological quality was evaluated using the Newcastle-Ottawa quality assessment scale adapted version. The results show that 27-30% of youngsters are at health "risk zone" for Body Mass Index (BMI), 70% for cardiorespiratory fitness (CRF), 50% and 65% for flexibility (FLEX) and muscular strength (MST), respectively. The data concerning skill-related fitness were inconsistent. In summary, the results suggest that Brazilian children and adolescents have low cardiovascular health level (BMI/CRF), mainly regarding CRF, and low muscle health level (FLEX/MST). We emphasize that the lack of studies regarding skill-related fitness, make it impossible to describe the profile of the components of this construct

O Projeto Esporte Brasil (PROESP-Br) propõe, desde 1994, uma bateria de medidas e testes para avaliação de escolares entre seis e 17 anos com o objetivo de delinear o perfil de crianças e jovens brasileiros no que se refere a aptidão física relacionada à saúde e ao desempenho motor. O objetivo deste estudo foi delinear o perfil da aptidão física de crianças e jovens brasileiros a partir de uma revisão sistemática da literatura sobre artigos que utilizaram da proposta do PROESP-Br. A busca foi realizada na PubMed, ScienceDirect, Lilacs, SciELO e Google Acadêmico. Estudos originais publicados entre 1994 e 2017 acerca da aptidão física (saúde e/ou desempenho motor) de escolares (crianças e/ou adolescentes) que utilizaram a bateria de testes do PROESP-Br foram incluídos. Um total de 13.582 sujeitos foram avaliados quanto a saúde e 276 quanto ao desempenho motor nos 18 estudos incluídos. A qualidade metodológica foi avaliada uma versão adaptada da Newcastle-Ottawa quality assessment scale. Os resultados evidenciam que 27-30% dos jovens estão na "zona de risco" à saúde para o Índice de Massa Corporal (IMC), 70% para a aptidão cardiorrespiratória (ApC) e 50 e 65% para flexibilidade e força muscular localizada (FML), respectivamente. Os dados sobre o desempenho motor são inconsistentes nesta revisão de literatura. Em síntese, os resultados indicam baixos níveis de saúde cardiovascular (IMC/ApC), principalmente quanto à ApC, assim como baixos níveis de saúde musculoesquelética (flexibilidade/FML) dos jovens. Ressalta-se a escassez de estudos quanto ao desempenho motor impossibilitando delinear o perfil dos componentes deste construto

Anthropometric characteristics, physical fitness components and technical skills, a comparison between Brazilian and Portuguese young soccer players / Características antropométricas, componentes de la aptitud física y habilidades técnicas, una comparación entre jóvenes futbolistas brasileños y portugueses / Comparação entre jovens futebolistas brasileiros e portugueses quanto às características morfológicas, funcionais e destreza motora

OBJECTIVE: Compare physical and technical performances and anthropometric characteristics between Brazilian and Portuguese young soccer players. METHOD: The participants were 281 Portuguese and 254 Brazilians from Under-15 and Under-17 categories. Measures were body weight and height, tests for strength, speed, agility, aerobic resistance, and a ball conduction drill as a motor skill test. RESULTS: Comparing Portuguese and Brazilian young soccer players from the same age, the European players presented a better anthropometric profile, physical fitness and motor skill than the Brazilians. CONCLUSIONS: Our hypothesis that the regular transferences from Brazilian players to Europe could suggest similar performances between the two competitive levels was not supported by the evidences

OBJETIVO: Comparar los desempeños físicos y técnicos y las características antropométricas entre los jugadores de fútbol jóvenes brasileños y portugueses. MÉTODO: Los participantes fueron 281 portugueses y 254 brasileños de las categorías sub-15 y sub-17. Mide el peso corporal y la altura, prueba de fuerza, velocidad, agilidad, resistencia aeróbica y un taladro de conducción de bolas como prueba de habilidad motora. RESULTADOS: Comparando futbolistas jóvenes portugueses y brasileños de la misma edad, los jugadores europeos presentaron un mejor perfil antropométrico, aptitud física y habilidad motora que los brasileños. CONCLUSIONES: Nuestra hipótesis de que las transferencias regulares de jugadores brasileños a Europa podrían sugerir desempeños similares entre los dos niveles competitivos no fue apoyada por las evidencias

OBJETIVO: Comparar as características antropométricas e o desempenho físico e técnico de jovens futebolistas brasileiros e portugueses. MÉTODO: Participaram do estudo 281 portugueses e 254 brasileiros das categorias sub-15 e sub-17. As medidas peso corporal e estatura, teste de força, velocidade, agilidade, resistência aeróbia e uma tarefa de condução de bola como teste de destreza motora. RESULTADOS: Ao comparar jovens portugueses e brasileiros da mesma faixa etária, os futebolistas europeus apresentaram melhor perfil antropométrico, aptidão física e destreza motora do que os brasileiros. CONCLUSÃO: Nossa hipótese de que as transferências regulares de jogadores brasileiros para a Europa poderiam sugerir desempenhos semelhantes entre os dois níveis competitivos não foram apoiados pelas evidências

The relative age effects in young soccer players and it relations with the competitive level, specific position, morphological characteristics, physical fitness and technical skills / O efeito da idade relativa em jovens futebolistas e suas relações com o nível de competição, posição específica, características morfológicas, capacidade física e habilidades técnicas / El efecto de la edad relativa de los futbolistas jóveves y si relación con el nivel de competencia, puesto específico, la morfología, la capacidad física y habilidades técnicas

This study investigated the relative age effects (RAE) in young soccer players and it relations to morphological, technical and physical variables, in a sample of 267 male players from U17 and U19 categories. Our results showed significant differences by age quartiles in relation to the competition level (U17), field positions (U17 and U19) and the 30m sprint test (U19). In summary, no significant associations were identified on morphological characteristics, physical fitness and technical skills in relation to the RAE.

Este estudo investigou o efeito da idade relativa (EIR) em jovens futebolistas e suas relações com variáveis morfológicas, técnicas e físicas em uma amostra de 267 jogadores de categorias Sub17 e Sub19. Nossos resultados mostraram diferenças significativas em função dos quartis etários em relação ao nível de competição (Sub17), posição de campo (Sub17 e Sub19) e teste de velocidade de 30m (Sub19). Em geral, nenhuma associação significativa foi identificada nas características morfológicas, capacidades físicas e habilidades técnicas em relação ao EIR.

Este estudio investigó el efecto de la edad relativa (EIR) en futbolistas jóvenes y su relación con variables morfológicas, técnicas y físicas en una muestra de 267 jugadores de las categorías Sub17 y Sub19. Nuestros resultados mostraron diferencias significativas según cuartiles de edad en comparación con el nivel de competencia (Sub17), la posición de campo (Sub17 y Sub19) y la prueba de velocidad de 30 metros (U19). En general, no hay asociación significativa fue identificado en las habilidades morfológicas, físicas y habilidades técnicas en relación con el EIR.

Educação Física Escolar: Percepções do Aluno com Deficiência1 / Physical Education: Disabled Students' Perceptions

RESUMO: a inclusão de alunos com deficiência é prevista em lei e manter boas estruturas físicas e pedagógicas na escola é um ponto fundamental para que o acesso possa acontecer. A Educação Física faz parte desta inclusão e pode proporcionar grandes melhoras na qualidade de vida de alunos com deficiência. Este estudo teve como objetivo compreender as percepções do aluno com deficiência a respeito das aulas de Educação Física. Para isso foi realizada uma pesquisa de natureza qualitativa utilizando para coleta de dados uma entrevista semiestruturada a qual foi gravada, transcrita e posteriormente analisada. A amostra foi constituída de 20 alunos com deficiência matriculados em escolas regulares da cidade de Santos Dumont - MG. A partir das entrevistas, destacou-se a percepção do aluno com deficiência a respeito da Educação Física escolar; o entendimento deles quanto ao conceito de qualidade de vida; as melhoras proporcionadas na qualidade de vida através da Educação Física; as facilidades e as dificuldades nas aulas; e as questões concernentes à relação aluno/professor e aluno/aluno. Os resultados dessa pesquisa podem auxiliar a comunidade escolar e o professor de Educação Física a melhorarem a inclusão nas escolas regulares. Além disso, as percepções dos alunos com deficiência sobre as aulas podem ajudar o professor na busca de um ambiente melhor com aulas que atendam a todos e proporcionem uma melhor qualidade de vida.

ABSTRACT: The inclusion of disabled students is based on the law and the adaptation of physical and pedagogical structure at school represents a key point in order to make the access happen. Physical education is a part of the social inclusion and can provide great improvements in quality of life of students with disabilities. This research aimed to verify the perception of the student with disabilities on physical education classes. Therefore, a qualitative research was carried out, using a semi structured interview to collect data. The interviews were recorded, transcribed and analyzed. The sample was constituted by 20 students with disabilities enrolled in general schools at Santos Dumont, Minas Gerais. From the interviews, we highlighted the perceptions of students with disabilities on physical education at school; their understanding about the concept of quality of life; the improvements provided in the quality of life through physical education; successes and difficulties in class; and issues concerning the relationship student/ teacher and student/student. The results of this research can help the educational community and the physical education teacher to improve the quality of inclusion in general schools. In addition, perceptions of students with disabilities about the lessons can help the teacher in the search for a better environment with classes that meet everyone's needs and provide a better of quality of life.

O futebol recreativo como uma nova abordagem terapêutica para a obesidade em crianças e adolescentes: uma revisão sistemática / Recreational soccer as a novel therapeutic approach to children and adolescent obesity: a systematic review

O aumento da prevalência de sobrepeso e obesidade tem se tornado um grave problema de saúde pública. No Brasil dados recentes sugerem que o sobrepeso atinge mais de 30% das crianças entre os cinco e os nove anos de idade e cerca de 20% da população entre os 10 e os 19 anos. A atividade física é considerada uma importante ferramenta para a prevenção e tratamento da obesidade infantil. O futebol, um dos desportos mais populares no mundo, tem sido considerado uma abordagem importante e eficaz para a promoção da saúde através da atividade física. O objetivo do presente estudo foi revisar o estado atual do conhecimento sobre a influência de programas de futebol recreativo (PFR) na prevenção e tratamento da obesidade e suas comorbidades associadas em crianças e adolescentes. Uma extensa pesquisa em bases de dados eletrônicas online foi realizada na Medline, ScienceDirect, LILACS, Scholar Google, Scopus e SPORTDiscus. Nove estudos preencheram todos os critérios de inclusão, com um total de 214 participantes que completaram seus respectivos programas de futebol recreativo. Embora um pequeno número de estudos tenha sido encontrado, os resultados reportados sugerem que a participação nos PFR pode melhorar a composição corporal, fatores de risco metabólicos e variáveis do bem-estar psicológico de crianças com sobrepeso e obesidade. Encontramos evidências de que a prática do futebol recreativo pode representar uma opção eficaz e acessível para a prevenção e tratamento da obesidade e suas comorbilidades associadas em crianças e adolescentes.

The raising level of overweight and obesity prevalence has become a serious public health problem. Recent Brazilian data suggest that overweight accounts for 30% of all children from five to nine years old and around 20% of the 10 to 19 population. Physical activity is considered an important tool for the prevention and treatment of child obesity. And soccer, one of the most popular sports in the world, has being considered and important and effective approach to promote health through physical activity, being yet of easy implementation and low investment. The objective of the present study was to review the current state of knowledge about the influence of recreational soccer programs (RSP) in the prevention and treatment of child and adolescent obesity and its associated comorbidities. An extensive search of online electronic databases was held in Medline, ScienceDirect, LILACS, Google Scholar, Scopus, and SPORTDiscus. Nine studies met all inclusion criteria for this review, with a total of 214 participants completing their respective recreational soccer program. Despite the low number of studies found, the reported results suggest that RSP's can improve the body composition profile, metabolic risk factors and psychological well-being variables of overweight and obese children. We found evidences that the practice of recreational soccer may represent an effective and available option to the prevention and treatment of obesity and it associated comorbidities in children and adolescents.