Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

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

Enthalpy–Entropy Compensation in Biomolecular Recognition: A Computational Perspective

(2021) Francesca Peccati et al.   ACS Omega

On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies

(2021) Vilhelm Ekberg et al.   Journal of Chemical Theory and Computation

Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA

(2020) Christopher J. Holland et al.   JOURNAL OF CLINICAL INVESTIGATION

T cell-engaging therapies — BiTEs and beyond

(2020) Maria-Elisabeth Goebeler et al.   Nature Reviews Clinical Oncology

Molecular rules underpinning enhanced affinity binding of human T cell receptors engineered for immunotherapy

(2020) Rory M. Crean et al.   Molecular Therapy-Oncolytics

Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations

(2019) Till Siebenmorgen et al.   Journal of Chemical Theory and Computation

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

(2019) David W. Wright et al.   Scientific Reports

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

(2019) Kamilla Kjærgaard Jensen et al.   Scientific Reports

Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies

(2018) Xiao Liu et al.   Journal of Chemical Theory and Computation

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

(2018) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

(2018) Irene Maffucci et al.   Frontiers in Chemistry

Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

(2018) Xiao Liu et al.   Journal of Chemical Information and Modeling

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design

(2018) Lance M. Hellman et al.   MOLECULAR THERAPY

Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity

(2017) Preeti Sharma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes

(2017) Dimas Suárez et al.   Journal of Chemical Information and Modeling

Interaction Entropy for Computational Alanine Scanning

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

Interaction entropy for protein-protein binding

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

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

(2017) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes

(2017) Nishant K. Singh et al.   JOURNAL OF IMMUNOLOGY

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1

(2017) Anthony J. Clark et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

(2016) Ozlem Keskin et al.   CHEMICAL REVIEWS

Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex

(2016) Daniel T. Harris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations

(2016) Vijayaraj Ramadoss et al.   Journal of Chemical Information and Modeling

Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method

(2016) Irene Maffucci et al.   Journal of Chemical Information and Modeling

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

(2016) Inês C. M. Simões et al.   Journal of Chemical Information and Modeling

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

(2016) Changhao Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

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

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach

(2014) Paulius Mikulskis et al.   JOURNAL OF MOLECULAR MODELING

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor

(2014) Brian G. Pierce et al.   PLoS Computational Biology

Increased peptide contacts govern high affinity binding of a modified TCR whilst maintaining a native pMHC docking mode

(2014) David Cole   Frontiers in Immunology

T-cell Receptor Specificity Maintained by Altered Thermodynamics

(2013) Florian Madura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations

(2013) Yong-Liang Zhu et al.   Journal of Chemical Information and Modeling

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Improved Generalized Born Solvent Model Parameters for Protein Simulations

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

Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes

(2013) Rui M. Ramos et al.   Journal of Chemical Theory and Computation

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

(2013) Sílvia A. Martins et al.   Journal of Chemical Theory and Computation

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations

(2013) Frithjof Godschalk et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structure-Based, Rational Design of T Cell Receptors

(2013) V. Zoete et al.   Frontiers in Immunology

ImmTACs

(2013) Joanne Oates et al.   OncoImmunology

Different affinity windows for virus and cancer-specific T-cell receptors: Implications for therapeutic strategies

(2012) Milos Aleksic et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

(2012) Samuel Genheden et al.   Journal of Chemical Information and Modeling

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Placevent: An algorithm for prediction of explicit solvent atom distribution-Application to HIV-1 protease and F-ATP synthase

(2012) Daniel J. Sindhikara et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes

(2012) Brian G. Pierce et al.   PROTEIN SCIENCE

COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes

(2011) A. Vangone et al.   BIOINFORMATICS

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

MM-GBSA binding free energy decomposition and T cell receptor engineering

(2010) V. Zoete et al.   JOURNAL OF MOLECULAR RECOGNITION

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

How to obtain statistically converged MM/GBSA results

(2009) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An improved method to predict the entropy term with the MM/PBSA approach

(2008) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Engineering higher affinity T cell receptors using a T cell display system

(2008) Adam S. Chervin et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC

(2008) Jaafar N. Haidar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS