Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Design and designability of protein-based assemblies

(2014) Jian Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Solvation Models: Theory and Validation

(2014) Enrico Purisima et al.   CURRENT PHARMACEUTICAL DESIGN

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

A comparison of various optimization algorithms of protein–ligand docking programs by fitness accuracy

(2014) Liyong Guo et al.   JOURNAL OF MOLECULAR MODELING

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

(2014) Sheng-You Huang et al.   NUCLEIC ACIDS RESEARCH

Specificity and affinity quantification of protein-protein interactions

(2013) Z. Yan et al.   BIOINFORMATICS

Automated docking for novel drug discovery

(2013) Martiniano Bello et al.   Expert Opinion on Drug Discovery

SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes

(2013) David Zilian et al.   Journal of Chemical Information and Modeling

Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

(2013) Zhiqiang Yan et al.   PLoS One

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

(2013) X. Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamic and kinetic specificities of ligand binding

(2013) Zhiqiang Yan et al.   Chemical Science

FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

(2012) Yu Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

(2012) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specificity quantification of biomolecular recognition and its implication for drug discovery

(2012) Zhiqiang Yan et al.   Scientific Reports

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions

(2011) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models

(2011) Anton Lindström et al.   Journal of Chemical Information and Modeling

Open Babel: An open chemical toolbox

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

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Virtual screening with AutoDock: theory and practice

(2010) Sandro Cosconati et al.   Expert Opinion on Drug Discovery

Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets

(2010) Christian Kramer et al.   Journal of Chemical Information and Modeling

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction

(2009) Yu Su et al.   PROTEIN SCIENCE

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

(2008) Bruce J. Berne et al.   Annual Review of Physical Chemistry

Metal-Coupled Folding of Cys2His2Zinc-Finger

(2007) Wenfei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY