Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation

Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy

(2021) Yan-jing Sheng et al.   Journal of Chemical Information and Modeling

Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi

(2020) Arghya Chakravorty et al.   Journal of Chemical Information and Modeling

How to measure and evaluate binding affinities

(2020) Inga Jarmoskaite et al.   eLife

Entropy of Proteins Using Multiscale Cell Correlation

(2020) Arghya Chakravorty et al.   Journal of Chemical Information and Modeling

Application and Comprehensive Analysis of Neighbor Approximated Information Theoretic Configurational Entropy Methods to Protein–Ligand Binding Cases

(2020) Shailesh Kumar Panday et al.   Journal of Chemical Theory and Computation

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

ISLAND: in-silico proteins binding affinity prediction using sequence information

(2020) Wajid Arshad Abbasi et al.   BioData Mining

Venetoclax in the treatment of chronic lymphocytic leukemia

(2019) Anna Korycka-Wolowiec et al.   Expert Opinion on Drug Metabolism & Toxicology

A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states

(2019) Tania Hazra et al.   JOURNAL OF MATHEMATICAL BIOLOGY

DelPhi Suite: New Developments and Review of Functionalities

(2019) Chuan Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational prediction of protein–protein binding affinities

(2019) Till Siebenmorgen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Hot-spot analysis for drug discovery targeting protein-protein interactions

(2018) Mireia Rosell et al.   Expert Opinion on Drug Discovery

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling

(2018) Arghya Chakravorty et al.   Journal of Chemical Theory and Computation

Atezolizumab for First-Line Treatment of Metastatic Nonsquamous NSCLC

(2018) Mark A. Socinski et al.   NEW ENGLAND JOURNAL OF MEDICINE

Interaction entropy for protein-protein binding

(2017) Zhaoxi Sun et al.   JOURNAL OF CHEMICAL PHYSICS

Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi

(2017) Zhe Jia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Durvalumab after Chemoradiotherapy in Stage III Non–Small-Cell Lung Cancer

(2017) Scott J. Antonia et al.   NEW ENGLAND JOURNAL OF MEDICINE

Protein–protein interactions: detection, reliability assessment and applications

(2016) Xiaoqing Peng et al.   BRIEFINGS IN BIOINFORMATICS

Current Experimental Methods for Characterizing Protein-Protein Interactions

(2016) Mi Zhou et al.   ChemMedChem

Pembrolizumab versus Chemotherapy for PD-L1–Positive Non–Small-Cell Lung Cancer

(2016) Martin Reck et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Nivolumab versus Docetaxel in Advanced Nonsquamous Non–Small-Cell Lung Cancer

(2015) Hossein Borghaei et al.   NEW ENGLAND JOURNAL OF MEDICINE

Contacts-based prediction of binding affinity in protein–protein complexes

(2015) Anna Vangone et al.   eLife

Antibody-Dependent Cellular Cytotoxicity Activity of a Novel Anti-PD-L1 Antibody Avelumab (MSB0010718C) on Human Tumor Cells

(2015) B. Boyerinas et al.   Cancer Immunology Research

Human protein interaction networks across tissues and diseases

(2015) Esti Yeger-Lotem et al.   Frontiers in Genetics

Protein–protein interactions and genetic diseases: The interactome

(2014) Kasper Lage   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Protein–protein binding affinity prediction from amino acid sequence

(2014) K. Yugandhar et al.   BIOINFORMATICS

CCharPPI web server: computational characterization of protein-protein interactions from structure

(2014) I. H. Moal et al.   BIOINFORMATICS

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

A functional feature analysis on diverse protein–protein interactions: application for the prediction of binding affinity

(2014) Jiesi Luo et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface

(2014) Panagiotis L. Kastritis et al.   JOURNAL OF MOLECULAR BIOLOGY

Direct methods for computing single-molecule entropies from molecular simulations

(2014) Dimas Suárez et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

Protein-protein interaction networks: probing disease mechanisms using model systems

(2013) Uros Kuzmanov et al.   Genome Medicine

Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding

(2012) F. Gaudreault et al.   BIOINFORMATICS

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

(2012) Junmei Wang et al.   Journal of Chemical Information and Modeling

Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation

(2012) Bracken M. King et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

Are Scoring Functions in Protein−Protein Docking Ready to Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Protein–protein interactions as targets for small-molecule therapeutics in cancer

(2008) Alex W. White et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE