Articles

Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling

Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specifi...

Authors: Tianyi Qiu, Dingfeng Wu, Jingxuan Qiu and Zhiwei Cao

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Kinases are major targets of anti-cancer therapies owing to their importance in signaling processes that regulate cell growth and proliferation. However, drug resistance has emerged as a major obstacle to canc...

Authors: Aeri Lee, Seungpyo Hong and Dongsup Kim

Finding the K best synthesis plans

In synthesis planning, the goal is to synthesize a target molecule from available starting materials, possibly optimizing costs such as price or environmental impact of the process. Current algorithmic approac...

Authors: Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle and Peter F. Stadler

A confidence predictor for logD using conformal regression and a support-vector machine

Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical c...

Authors: Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson and Ola Spjuth

The dye-sensitized solar cell database

Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, e...

Authors: Vishwesh Venkatraman, Rajesh Raju, Solon P. Oikonomopoulos and Bjørn K. Alsberg

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to b...

Authors: Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen and Dong-Sheng Cao

A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening

Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerpr...

Authors: Julia B. Jasper, Lina Humbeck, Tobias Brinkjost and Oliver Koch

Comment on “The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability”

Authors: M. Šícho, M. Voršilák and D. Svozil

Reply to the comment made by Šicho, Vorśilák and Svozil on ‘The Power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability’

Authors: Hans De Winter and Julio Cesar Dias Lopes

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors

A number of anti-retroviral drugs are being used for treating Human Immunodeficiency Virus (HIV) infection. Due to emergence of drug resistant strains, there is a constant quest to discover more effective anti...

Authors: Abid Qureshi, Akanksha Rajput, Gazaldeep Kaur and Manoj Kumar

Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics

Both the automated generation of reaction networks and the automated prediction of synthetic trees require, in one way or another, the definition of possible transformations a molecule can undergo. One way of ...

Authors: Pieter P. Plehiers, Guy B. Marin, Christian V. Stevens and Kevin M. Van Geem

OPERA models for predicting physicochemical properties and environmental fate endpoints

The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public...

Authors: Kamel Mansouri, Chris M. Grulke, Richard S. Judson and Antony J. Williams

Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening

Spectrophores are novel descriptors that are calculated from the three-dimensional atomic properties of molecules. In our current implementation, the atomic properties that were used to calculate spectrophores...

Authors: Rafaela Gladysz, Fabio Mendes Dos Santos, Wilfried Langenaeker, Gert Thijs, Koen Augustyns and Hans De Winter

Efficient iterative virtual screening with Apache Spark and conformal prediction

Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out ...

Authors: Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Toor, Wesley Schaal, Erwin Laure and Ola Spjuth

Maximizing gain in high-throughput screening using conformal prediction

Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, ...

Authors: Fredrik Svensson, Avid M. Afzal, Ulf Norinder and Andreas Bender

Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies

Given that many antifungal medications are susceptible to evolved resistance, there is a need for novel drugs with unique mechanisms of action. Inhibiting the essential proton pump Pma1p, a P-type ATPase, is a...

Authors: Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki and Jacob D. Durrant

Key features and updates for Origin 2018

OriginLab’s newest version update to Origin and OriginPro includes ease-of-use features, like Origin Central updates and creation of an App Center, as well as larger changes like the addition of Unicode charac...

Authors: James G. Moberly, Matthew T. Bernards and Kristopher V. Waynant

Mordred: a molecular descriptor calculator

Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those progra...

Authors: Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita and Tatsuya Takagi

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking

Idiosyncratic adverse drug reactions have been linked to a drug’s ability to bind with a human leukocyte antigen (HLA) protein. However, due to the thousands of HLA variants and limited structural data for dru...

Authors: George Van Den Driessche and Denis Fourches

3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein–ligand interactions

Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, inclu...

Authors: Sehan Lee and Mace G. Barron

An automated framework for QSAR model building

In-silico quantitative structure–activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules base...

Authors: Samina Kausar and Andre O. Falcao

Computer-aided design of multi-target ligands at A₁R, A_2AR and PDE10A, key proteins in neurodegenerative diseases

Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may ...

Authors: Leen Kalash, Cristina Val, Jhonny Azuaje, María I. Loza, Fredrik Svensson, Azedine Zoufir, Lewis Mervin, Graham Ladds, José Brea, Robert Glen, Eddy Sotelo and Andreas Bender

Systematic exploration of multiple drug binding sites

Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple bin...

Authors: Mónika Bálint, Norbert Jeszenői, István Horváth, David van der Spoel and Csaba Hetényi

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for...

Authors: Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu and Tingjun Hou

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a s...

Authors: Mathilde Koch, Thomas Duigou, Pablo Carbonell and Jean-Loup Faulon