USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

UFSRAT: Ultra-Fast Shape Recognition with Atom Types –The Discovery of Novel Bioactive Small Molecular Scaffolds for FKBP12 and 11βHSD1

(2015) Steven Shave et al.   PLoS One

Structure- and Ligand-Based Virtual Screening Identifies New Scaffolds for Inhibitors of the Oncoprotein MDM2

(2015) Douglas R. Houston et al.   PLoS One

iview: an interactive WebGL visualizer for protein-ligand complex

(2014) Hongjian Li et al.   BMC BIOINFORMATICS

Biochemical evaluation of virtual screening methods reveals a cell-active inhibitor of the cancer-promoting phosphatases of regenerating liver

(2014) Birgit Hoeger et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Prospective virtual screening for novel p53–MDM2 inhibitors using ultrafast shape recognition

(2014) Sachin P. Patil et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A multi-fingerprint browser for the ZINC database

(2014) Mahendra Awale et al.   NUCLEIC ACIDS RESEARCH

istar: A Web Platform for Large-Scale Protein-Ligand Docking

(2014) Hongjian Li et al.   PLoS One

A new method for rapid comparison of protein binding pockets by capturing spatial distributions

(2014) Timo Krotzky et al.   Journal of Cheminformatics

ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method

(2013) Jiayu Gong et al.   BIOINFORMATICS

Scaffold Hopping by Fragment Replacement

(2013) Mikko J. Vainio et al.   Journal of Chemical Information and Modeling

PDBe: Protein Data Bank in Europe

(2013) Aleksandras Gutmanas et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Adenosiland: Walking through adenosine receptors landscape

(2012) Matteo Floris et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Freely Available Conformer Generation Methods: How Good Are They?

(2012) Jean-Paul Ebejer et al.   Journal of Chemical Information and Modeling

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

(2012) P. J. Ballester et al.   Journal of the Royal Society Interface

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints

(2012) Adrian M Schreyer et al.   Journal of Cheminformatics

Similarity methods in chemoinformatics

(2011) Peter Willett   ANNUAL REVIEW OF INFORMATION SCIENCE AND TECHNOLOGY

Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening

(2011) Li Xing et al.   JOURNAL OF MEDICINAL CHEMISTRY

Swimming into peptidomimetic chemical space using pepMMsMIMIC

(2011) M. Floris et al.   NUCLEIC ACIDS RESEARCH

Advances in Cheminformatics Methodologies and Infrastructure to Support the Data Mining of Large, Heterogeneous Chemical Datasets

(2010) Rajarshi Guha et al.   Current Computer-Aided Drug Design

Ultrafast shape recognition: method and applications

(2010) Pedro J Ballester   Future Medicinal Chemistry

Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration

(2010) Amarda Shehu et al.   INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH

ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics

(2010) M. Stuart Armstrong et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

(2010) Peter Ripphausen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Complementing ultrafast shape recognition with an optical isomerism descriptor

(2010) Ting Zhou et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Frog2: Efficient 3D conformation ensemble generator for small compounds

(2010) M. A. Miteva et al.   NUCLEIC ACIDS RESEARCH

EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities

(2010) Kun-Yi Hsin et al.   NUCLEIC ACIDS RESEARCH

Tracing conformational changes in proteins

(2010) Nurit Haspel et al.   BMC STRUCTURAL BIOLOGY

WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications

(2010) Qian Zhu et al.   Journal of Cheminformatics

BIPA: a database for protein–nucleic acid interaction in 3D structures

(2009) Semin Lee et al.   BIOINFORMATICS

CREDO: A Protein-Ligand Interaction Database for Drug Discovery

(2009) Adrian Schreyer et al.   Chemical Biology & Drug Design

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Novel Approach for Chemotype Hopping Based on Annotated Databases of Chemically Feasible Fragments and a Prospective Case Study: New Melanin Concentrating Hormone Antagonists

(2009) Julen Oyarzabal et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of Novel Falcipain-2 Inhibitors as Potential Antimalarial Agents through Structure-Based Virtual Screening

(2009) Honglin Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology

(2009) Pedro J. Ballester et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases

(2009) P. J. Ballester et al.   Journal of the Royal Society Interface

Identification of a chemical probe for NAADP by virtual screening

(2009) Edmund Naylor et al.   Nature Chemical Biology

The importance of discerning shape in molecular pharmacology

(2009) Sandhya Kortagere et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Discovery of Novel PPAR Ligands by a Virtual Screening Approach Based on Pharmacophore Modeling, 3D Shape, and Electrostatic Similarity Screening

(2008) Patrick Markt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Multiscale Approach to Explore the Potential Energy Surface of Water Clusters (H2O)nn≤ 8

(2008) Quoc Chinh Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY A