Finding Druggable Sites in Proteins Using TACTICS

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

(2020) Antonija Kuzmanic et al.   ACCOUNTS OF CHEMICAL RESEARCH

Druggability Assessment in TRAPP using Machine Learning Approaches

(2020) Jui-Hung Yuan et al.   Journal of Chemical Information and Modeling

Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)

(2020) Alexander D. MacKerell et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin et al.   NATURE

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy

(2020) Bhupesh Goyal et al.   ACS Combinatorial Science

D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19

(2020) Yulong Shi et al.   Acta Pharmaceutica Sinica B

SARS-CoV-2 Main Protease: A Molecular Dynamics Study

(2020) Dimas Suárez et al.   Journal of Chemical Information and Modeling

Structural basis of RNA cap modification by SARS-CoV-2

(2020) Thiruselvam Viswanathan et al.   Nature Communications

Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin

(2020) Petra Krafcikova et al.   Nature Communications

Allosteric Inhibition of the SARS‐CoV‐2 Main Protease: Insights from Mass Spectrometry Based Assays

(2020) Tarick J. El‐Baba et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-resolution structures of the SARS-CoV-2 2′-O-methyltransferase reveal strategies for structure-based inhibitor design

(2020) Monica Rosas-Lemus et al.   Science Signaling

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

(2020) Alice Douangamath et al.   Nature Communications

Protein Flexibility and Stiffness Enable Efficient Enzymatic Catalysis

(2019) John P. Richard   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling

(2019) Justin R. Porter et al.   BIOPHYSICAL JOURNAL

D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics

(2019) Zhaoqiang Chen et al.   Journal of Chemical Information and Modeling

Discovery of novel allosteric site and covalent inhibitors of FBPase with potent hypoglycemic effects

(2019) Yunyuan Huang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Cryptic binding sites on proteins: definition, detection, and druggability

(2018) Sandor Vajda et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations

(2018) Sarah E. Graham et al.   Journal of Chemical Information and Modeling

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH

(2018) Federico Comitani et al.   Journal of Chemical Theory and Computation

Exploring the structural origins of cryptic sites on proteins

(2018) Dmitri Beglov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NanoShaper–VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems

(2018) Sergio Decherchi et al.   BIOINFORMATICS

Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication

(2017) Andrew C. Goodrich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics

(2017) S. Roy Kimura et al.   Journal of Chemical Information and Modeling

POVME 3.0: Software for Mapping Binding Pocket Flexibility

(2017) Jeffrey R. Wagner et al.   Journal of Chemical Theory and Computation

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

(2017) Antonia Stank et al.   NUCLEIC ACIDS RESEARCH

Systematic exploration of multiple drug binding sites

(2017) Mónika Bálint et al.   Journal of Cheminformatics

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

(2017) Giuseppina La Sala et al.   ACS Central Science

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

(2016) Peter Cimermancic et al.   JOURNAL OF MOLECULAR BIOLOGY

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems

(2016) Phani Ghanakota et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

(2016) Vladimiras Oleinikovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding of the Methyl Donor S -Adenosyl-l-Methionine to Middle East Respiratory Syndrome Coronavirus 2′- O -Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10

(2016) Wahiba Aouadi et al.   JOURNAL OF VIROLOGY

A Collective Variable for the Rapid Exploration of Protein Druggability

(2015) Rémi Cuchillo et al.   Journal of Chemical Theory and Computation

Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts

(2015) Andrew C. Goodrich et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features

(2015) Radoslav Krivák et al.   Journal of Cheminformatics

ENCORE: Software for Quantitative Ensemble Comparison

(2015) Matteo Tiberti et al.   PLoS Computational Biology

Epock: rapid analysis of protein pocket dynamics

(2014) Benoist Laurent et al.   BIOINFORMATICS

KVFinder: steered identification of protein cavities as a PyMOL plugin

(2014) Saulo HP Oliveira et al.   BMC BIOINFORMATICS

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

(2014) Jacob D. Durrant et al.   Journal of Chemical Theory and Computation

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity

(2014) Teresa Paramo et al.   Journal of Chemical Theory and Computation

GalaxySite: ligand-binding-site prediction by using molecular docking

(2014) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

(2013) Daria B. Kokh et al.   Journal of Chemical Information and Modeling

A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

(2013) Sergio Decherchi et al.   PLoS One

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

(2012) Ahmet Bakan et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

(2011) Peter Schmidtke et al.   BIOINFORMATICS

Combining Global and Local Measures for Structure-Based Druggability Predictions

(2011) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

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

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Open Babel: An open chemical toolbox

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

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

(2010) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

POVME: An algorithm for measuring binding-pocket volumes

(2010) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

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

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Detection of multiscale pockets on protein surfaces using mathematical morphology

(2009) Takeshi Kawabata   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY