SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction

SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

(2021) Martin Amezcua et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

(2021) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge

(2021) Teresa Danielle Bergazin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GNINA 1.0: molecular docking with deep learning

(2021) Andrew T. McNutt et al.   Journal of Cheminformatics

Octanol–water partition coefficient measurements for the SAMPL6 blind prediction challenge

(2020) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge

(2020) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex

(2020) David de Semir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowdsourcing drug discovery for pandemics

(2020) John Chodera et al.   Nature Chemistry

What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen?

(2020) Aled Edwards   Journal of Chemical Information and Modeling

spyrmsd: symmetry-corrected RMSD calculations in Python

(2020) Rocco Meli et al.   Journal of Cheminformatics

Generating multibillion chemical space of readily accessible screening compounds

(2020) Oleksandr O. Grygorenko et al.   iScience

The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting

(2020) Nathan David Wright et al.   Acta Crystallographica Section D-Structural Biology

FragLites—Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation

(2019) Daniel J. Wood et al.   JOURNAL OF MEDICINAL CHEMISTRY

A bright future for fragment-based drug discovery: what does it hold?

(2019) Célien Jacquemard et al.   Expert Opinion on Drug Discovery

Bromodomain biology and drug discovery

(2019) Nilesh Zaware et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computational Fragment-Based Drug Design: Current Trends, Strategies, and Applications

(2018) Yuemin Bian et al.   AAPS Journal

PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer

(2018) David de Semir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

(2018) Mehtap Işık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations

(2017) Gerard Martínez-Rosell et al.   Journal of Chemical Information and Modeling

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database

(2017) Richard J. Hall et al.   JOURNAL OF MEDICINAL CHEMISTRY

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density

(2017) Nicholas M. Pearce et al.   Nature Communications

TheXChemExplorergraphical workflow tool for routine or large-scale protein–ligand structure determination

(2017) Tobias Krojer et al.   Acta Crystallographica Section D-Structural Biology

Gentle, fast and effective crystal soaking by acoustic dispensing

(2017) Patrick M. Collins et al.   Acta Crystallographica Section D-Structural Biology

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

(2016) Shipra Malhotra et al.   JOURNAL OF MEDICINAL CHEMISTRY

Dynamic undocking and the quasi-bound state as tools for drug discovery

(2016) Sergio Ruiz-Carmona et al.   Nature Chemistry

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits

(2016) Johannes Schiebel et al.   STRUCTURE

A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain

(2016) Oakley B. Cox et al.   Chemical Science

Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo

(2015) Gregory A. Ross et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DIMPLE- a pipeline for the rapid generation of difference maps from protein crystals with putatively bound ligands

(2015) Marcin Wojdyr et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Blind prediction of HIV integrase binding from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

(2014) Thomas S. Peat et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

(2014) Daniel Alvarez-Garcia et al.   JOURNAL OF MEDICINAL CHEMISTRY

Advantages of crystallographic fragment screening: Functional and mechanistic insights from a powerful platform for efficient drug discovery

(2014) Disha Patel et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Using textons to rank crystallization droplets by the likely presence of crystals

(2014) Jia Tsing Ng et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Fragment Based Drug Design: From Experimental to Computational Approaches

(2012) A. Kumar et al.   CURRENT MEDICINAL CHEMISTRY

A fragment-based approach to the SAMPL3 Challenge

(2012) John L. Kulp et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

(2012) Gregory A. Ross et al.   PLoS One

Pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis

(2012) D. De Semir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Study of the Complex Stereoselectivity of Human Butyrylcholinesterase for the Neurotoxic V-agents

(2011) Marielle Wandhammer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The DINGO dataset: a comprehensive set of data for the SAMPL challenge

(2011) Janet Newman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Open Babel: An open chemical toolbox

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

Structure and function of WD40 domain proteins

(2011) Chao Xu et al.   Protein & Cell

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The full-length isoform of the mouse pleckstrin homology domain-interacting protein (PHIP) is required for postnatal growth

(2010) Shuai Li et al.   FEBS LETTERS

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

SAMPL2 challenge: prediction of solvation energies and tautomer ratios

(2010) A. Geoffrey Skillman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The rise of fragment-based drug discovery

(2009) Christopher W. Murray et al.   Nature Chemistry

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Ligand−Protein Docking with Water Molecules

(2008) Benjamin C. Roberts et al.   Journal of Chemical Information and Modeling