AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization

LigBuilder V3: A Multi-Target de novo Drug Design Approach

(2020) Yaxia Yuan et al.   Frontiers in Chemistry

In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery

(2020) Lauro Ribeiro de Souza Neto et al.   Frontiers in Chemistry

Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

(2019) Patrick J. Ropp et al.   Journal of Cheminformatics

Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins

(2019) Elizaveta E Alemasova et al.   NUCLEIC ACIDS RESEARCH

Design and Synthesis of Poly(ADP-ribose) Polymerase Inhibitors: Impact of Adenosine Pocket-Binding Motif Appendage to the 3-Oxo-2,3-dihydrobenzofuran-7-carboxamide on Potency and Selectivity

(2019) Uday Kiran Velagapudi et al.   JOURNAL OF MEDICINAL CHEMISTRY

MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design

(2019) Chu et al.   MOLECULES

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

(2019) Patrick J. Ropp et al.   Journal of Cheminformatics

FDA Approval Summary: Niraparib for the Maintenance Treatment of Patients with Recurrent Ovarian Cancer in Response to Platinum-Based Chemotherapy

(2018) Gwynn Ison et al.   CLINICAL CANCER RESEARCH

Design and synthesis of 2-(4,5,6,7-tetrahydrothienopyridin-2-yl)-benzoimidazole carboxamides as novel orally efficacious Poly(ADP-ribose)polymerase (PARP) inhibitors

(2018) Xuxing Chen et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Conditional molecular design with deep generative models

(2018) Seokho Kang et al.   Journal of Chemical Information and Modeling

BlendMol: advanced macromolecular visualization in Blender

(2018) Jacob D Durrant   BIOINFORMATICS

Talazoparib: First Global Approval

(2018) Sheridan M. Hoy   DRUGS

PARP inhibitors: Clinical utility and possibilities of overcoming resistance

(2017) Benjamin G. Bitler et al.   GYNECOLOGIC ONCOLOGY

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

(2017) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Scoria: a Python module for manipulating 3D molecular data

(2017) Patrick Ropp et al.   Journal of Cheminformatics

Molecular de-novo design through deep reinforcement learning

(2017) Marcus Olivecrona et al.   Journal of Cheminformatics

AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization

(2016) Yan Li et al.   Journal of Chemical Information and Modeling

Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors

(2016) Ann-Gerd Thorsell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Blocking c-Met–mediated PARP1 phosphorylation enhances anti-tumor effects of PARP inhibitors

(2016) Yi Du et al.   NATURE MEDICINE

Crystal structure-based discovery of a novel synthesized PARP1 inhibitor (OL-1) with apoptosis-inducing mechanisms in triple-negative breast cancer

(2016) Leilei Fu et al.   Scientific Reports

Fast, accurate, and reliable molecular docking with QuickVina 2

(2015) Amr Alhossary et al.   BIOINFORMATICS

FDA Approval Summary: Olaparib Monotherapy in Patients with Deleterious Germline BRCA-Mutated Advanced Ovarian Cancer Treated with Three or More Lines of Chemotherapy

(2015) G. Kim et al.   CLINICAL CANCER RESEARCH

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery of 2-[1-(4,4-Difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide (NMS-P118): A Potent, Orally Available, and Highly Selective PARP-1 Inhibitor for Cancer Therapy

(2015) Gianluca Papeo et al.   JOURNAL OF MEDICINAL CHEMISTRY

PARP-1 Activation Requires Local Unfolding of an Autoinhibitory Domain

(2015) Jennine M. Dawicki-McKenna et al.   MOLECULAR CELL

A unified lead-oriented synthesis of over fifty molecular scaffolds

(2015) Richard G. Doveston et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

(2015) Dávid Bajusz et al.   Journal of Cheminformatics

Improving clinical outcomes – towards patient-centred laboratory medicine

(2015) Mike J Hallworth   ANNALS OF CLINICAL BIOCHEMISTRY

Discovery and Structure–Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors

(2014) Maulik R. Patel et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN 673, a potent inhibitor derived from dihydropyridophthalazinone

(2014) Mika Aoyagi-Scharber et al.   Acta Crystallographica Section F-Structural Biology Communications

PARP Inhibitor with Selectivity Toward ADP-Ribosyltransferase ARTD3/PARP3

(2013) Anders E. G. Lindgren et al.   ACS Chemical Biology

De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach

(2013) Kentaro Kawai et al.   Journal of Chemical Information and Modeling

Estimation of the size of drug-like chemical space based on GDB-17 data

(2013) P. G. Polishchuk et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Design, Synthesis, and Biological Evaluation of a Series of Benzo[de][1,7]naphthyridin-7(8H)-ones Bearing a Functionalized Longer Chain Appendage as Novel PARP1 Inhibitors

(2013) Na Ye et al.   JOURNAL OF MEDICINAL CHEMISTRY

AutoGrow 3.0: An improved algorithm for chemically tractable, semi-automated protein inhibitor design

(2013) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders

(2012) Steffen Lindert et al.   Chemical Biology & Drug Design

Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors

(2012) Elisabet Wahlberg et al.   NATURE BIOTECHNOLOGY

AutoClickChem: Click Chemistry in Silico

(2012) Jacob D. Durrant et al.   PLoS Computational Biology

PARP regulates nonhomologous end joining through retention of Ku at double-strand breaks

(2011) C. Anne-Marie Couto et al.   JOURNAL OF CELL BIOLOGY

A Collection of Robust Organic Synthesis Reactions forIn SilicoMolecule Design

(2011) Markus Hartenfeller et al.   Journal of Chemical Information and Modeling

LigBuilder 2: A Practicalde NovoDrug Design Approach

(2011) Yaxia Yuan et al.   Journal of Chemical Information and Modeling

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

BINANA: A novel algorithm for ligand-binding characterization

(2011) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Nonhomologous end joining drives poly(ADP-ribose) polymerase (PARP) inhibitor lethality in homologous recombination-deficient cells

(2011) A. G. Patel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes

(2010) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

(2010) Jonathan B. Baell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina

(2010) Max W. Chang et al.   PLoS One

AutoGrow: A Novel Algorithm for Protein Inhibitor Design

(2009) Jacob D. Durrant et al.   Chemical Biology & Drug Design

E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization

(2009) Bradley C. Pearce et al.   Journal of Chemical Information and Modeling

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Quantitative Analyses of Aggregation, Autofluorescence, and Reactivity Artifacts in a Screen for Inhibitors of a Thiol Protease

(2009) Ajit Jadhav et al.   JOURNAL OF MEDICINAL CHEMISTRY

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

(2008) Muralidhar L Hegde et al.   CELL RESEARCH

On the Art of Compiling and Using 'Drug-Like' Chemical Fragment Spaces

(2008) Jörg Degen et al.   ChemMedChem

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

Ligand Binding Efficiency: Trends, Physical Basis, and Implications

(2008) Charles H. Reynolds et al.   JOURNAL OF MEDICINAL CHEMISTRY

Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases

(2007) Ruth Brenk et al.   ChemMedChem

MPI for Python: Performance improvements and MPI-2 extensions

(2007) Lisandro Dalcín et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING