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

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

(2014) Wenbo Yu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

How proteins bind macrocycles

(2014) Elizabeth A Villar et al.   Nature Chemical Biology

PredHS: a web server for predicting protein–protein interaction hot spots by using structural neighborhood properties

(2014) Lei Deng et al.   NUCLEIC ACIDS RESEARCH

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

(2014) Tanggis Bohnuud et al.   PLoS Computational Biology

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

(2013) Laurie E. Grove et al.   BIOINFORMATICS

GAMESS As a Free Quantum-Mechanical Platform for Drug Research

(2013) Yuri Alexeev et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

(2013) Katrina W. Lexa et al.   Journal of Chemical Information and Modeling

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

(2013) E. Prabhu Raman et al.   Journal of Chemical Information and Modeling

Multistructural hot spot characterization with FTProd

(2012) Lane Votapka et al.   BIOINFORMATICS

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces

(2012) Brandon S. Zerbe 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

Ordering of the N-Terminus of Human MDM2 by Small Molecule Inhibitors

(2012) Klaus Michelsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

(2012) Tanggis Bohnuud et al.   NUCLEIC ACIDS RESEARCH

FTMAP: extended protein mapping with user-selected probe molecules

(2012) C. H. Ngan et al.   NUCLEIC ACIDS RESEARCH

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery

(2011) David R. Hall et al.   Journal of Chemical Information and Modeling

Protein Hot Spots: The Islands of Stability

(2011) Yosef Y. Kuttner et al.   JOURNAL OF MOLECULAR BIOLOGY

Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme

(2011) David H. Hall et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural conservation of druggable hot spots in protein-protein interfaces

(2011) D. Kozakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimal ensembles of side chain conformers for modeling protein-protein interactions

(2011) Dmitri Beglov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features

(2011) Xiaolei Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Confab - Systematic generation of diverse low-energy conformers

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

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ryan Brenke et al.   BIOINFORMATICS

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

(2009) Nurcan Tuncbag et al.   BIOINFORMATICS

Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel

(2009) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

(2009) Melissa R. Landon et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

SITEHOUND-web: a server for ligand binding site identification in protein structures

(2009) M. Hernandez et al.   NUCLEIC ACIDS RESEARCH

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

(2009) Michelle Dechene et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble

(2008) Melissa R. Landon et al.   Chemical Biology & Drug Design