Human leukocyte antigen (HLA) surface proteins are directly involved in idiosyncratic adverse drug reactions. Herein, we present a structure-based analysis of the common HLA-B*57:01 variant known to be respons...
Authors: George Van Den Driessche and Denis Fourches
A large proportion of polar anthropogenic compounds routinely released into the environment comprises homologue series, i.e., sets of chemicals differing in a repeating chemical unit. Using analytical techniq...
Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictio...
The symbols for the new IUPAC elements named in November 2016 can introduce subtle ambiguities within cheminformatics software. The ambiguities are described and demonstrated by highlighting inconsistencies be...
Molecular fingerprints are widely used in several areas of chemoinformatics including diversity analysis and similarity searching. The fingerprint-based analysis of chemical libraries, in particular of large c...
Authors: Eli Fernández-de Gortari, César R. García-Jacas, Karina Martinez-Mayorga and José L. Medina-Franco
A new metric for the evaluation of model performance in the field of virtual screening and quantitative structure–activity relationship applications is described. This metric has been termed the power metric a...
Authors: Julio Cesar Dias Lopes, Fábio Mendes dos Santos, Andrelly Martins-José, Koen Augustyns and Hans De Winter
Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an im...
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and p...
Authors: Sandip De, Felix Musil, Teresa Ingram, Carsten Baldauf and Michele Ceriotti
Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. Th...
Authors: Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin and Chun-Wei Tung
The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with Dat...
Authors: Matthew J. Harvey, Andrew McLean and Henry S. Rzepa
Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molec...
Authors: Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N. Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo and Emanuele Amata
Molecular descriptors have been widely used to predict biological activities and physicochemical properties or to analyze chemical libraries on the basis of similarity. Although fingerprints and properties are...
Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a compr...
Authors: Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo and Hwangseo Park
Visualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern method...
Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, g...
Authors: Muthukumarasamy Karthikeyan and Renu Vyas
Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligom...
Authors: Saw Simeon, Watshara Shoombuatong, Nuttapat Anuwongcharoen, Likit Preeyanon, Virapong Prachayasittikul, Jarl E. S. Wikberg and Chanin Nantasenamat
Acquired immune deficiency syndrome is a deadly disease which is caused by human immunodeficiency virus (HIV). This virus attacks patients immune system and effects its ability to fight against diseases. Deve...
Authors: Yunuscan Koçak, Tansel Özyer and Reda Alhajj
Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan protein...
Authors: Joshua Meyers, Nathan Brown and Julian Blagg
The ability to define the regions of chemical space where a predictive model can be safely used is a necessary condition to assure the reliability of new predictions. This implies that reliability must be dete...
Authors: Natália Aniceto, Alex A. Freitas, Andreas Bender and Taravat Ghafourian
The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site o...
Authors: Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov and Vladimir V. Poroikov
Predictive modelling in drug discovery is challenging to automate as it often contains multiple analysis steps and might involve cross-validation and parameter tuning that create complex dependencies between ...
Authors: Samuel Lampa, Jonathan Alvarsson and Ola Spjuth
Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious....
Authors: Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie and Jason E. Bara
The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution im...
Authors: Hugo López-Fernández, Gustavo de S. Pessôa, Marco A. Z. Arruda, José L. Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña and Miguel Reboiro-Jato
Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitabl...
Authors: Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic
Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinfor...
Authors: Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen and José L. Medina-Franco