AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

Recognizing metal and acid radical ion-binding sites by integratingab initiomodeling with template-based transferals

(2016) Xiuzhen Hu et al.   BIOINFORMATICS

Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands

(2016) Stefan G. Krimmer et al.   JOURNAL OF MEDICINAL CHEMISTRY

3Drefine: an interactive web server for efficient protein structure refinement

(2016) Debswapna Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

CSM-lig: a web server for assessing and comparing protein–small molecule affinities

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Hongjian Li et al.   NUCLEIC ACIDS RESEARCH

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

(2015) Francesca Spyrakis et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Building a virtual ligand screening pipeline using free software: a survey

(2015) Enrico Glaab   BRIEFINGS IN BIOINFORMATICS

FAF-Drugs3: a web server for compound property calculation and chemical library design

(2015) David Lagorce et al.   NUCLEIC ACIDS RESEARCH

MTiOpenScreen: a web server for structure-based virtual screening

(2015) Céline M. Labbé et al.   NUCLEIC ACIDS RESEARCH

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

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

One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade

(2013) Bruno O. Villoutreix et al.   DRUG DISCOVERY TODAY

How far can virtual screening take us in drug discovery?

(2013) Supratik Kar et al.   Expert Opinion on Drug Discovery

CovalentDock Cloud: a web server for automated covalent docking

(2013) Xuchang Ouyang et al.   NUCLEIC ACIDS RESEARCH

Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality

(2013) Hardik I. Parikh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognizing Pitfalls in Virtual Screening: A Critical Review

(2012) Thomas Scior et al.   Journal of Chemical Information and Modeling

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

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

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

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

(2012) Chih-Hao Lu et al.   PLoS One

Structure-based drug design to augment hit discovery

(2011) Subha Kalyaanamoorthy et al.   DRUG DISCOVERY TODAY

iScreen: world’s first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

(2011) Tsung-Ying Tsai et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SwissDock, a protein-small molecule docking web service based on EADock DSS

(2011) A. Grosdidier et al.   NUCLEIC ACIDS RESEARCH

The Role of Water Molecules in Computational Drug Design

(2010) Stephanie de Beer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-Score and FRED scoring functions

(2010) Tania Pencheva et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

e-LEA3D: a computational-aided drug design web server

(2010) D. Douguet   NUCLEIC ACIDS RESEARCH

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Automated Docking Screens: A Feasibility Study

(2009) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

(2008) Tania Pencheva et al.   BMC BIOINFORMATICS

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

(2008) Alessio Amadasi et al.   JOURNAL OF MEDICINAL CHEMISTRY