SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity

Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks

(2016) Zhiqiang Yan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Non-coding RNAs as drug targets

(2016) Masayuki Matsui et al.   NATURE REVIEWS DRUG DISCOVERY

Studying non-covalent drug–DNA interactions

(2015) Sayeed Ur Rehman et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

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

(2015) Zhiqiang Yan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Specificity and affinity quantification of protein-protein interactions

(2013) Z. Yan et al.   BIOINFORMATICS

Structure-Based DNA-Targeting Strategies with Small Molecule Ligands for Drug Discovery

(2013) Jia Sheng et al.   MEDICINAL RESEARCH REVIEWS

MicroRNAs and other non-coding RNAs as targets for anticancer drug development

(2013) Hui Ling et al.   NATURE REVIEWS DRUG DISCOVERY

The Nucleic Acid Database: new features and capabilities

(2013) Buvaneswari Coimbatore Narayanan et al.   NUCLEIC ACIDS RESEARCH

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

LigandRNA: computational predictor of RNA-ligand interactions

(2013) A. Philips et al.   RNA

Thermodynamic and kinetic specificities of ligand binding

(2013) Zhiqiang Yan et al.   Chemical Science

Nucleic acid aptamers: an emerging frontier in cancer therapy

(2012) Guizhi Zhu et al.   CHEMICAL COMMUNICATIONS

Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery

(2012) Lu Chen et al.   Journal of Chemical Information and Modeling

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Gevorg Grigoryan et al.   NATURE

Ligand binding to nucleic acids and proteins: Does selectivity increase with strength?

(2008) Hans-Jörg Schneider   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA

(2008) Xiaoyu Zhao et al.   Journal of Chemical Information and Modeling

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS