CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

(2021) Ya Gao et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

(2021) Han Zhang et al.   Journal of Chemical Information and Modeling

CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement

(2021) Hugo Guterres et al.   Journal of Chemical Information and Modeling

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations

(2020) Hugo Guterres et al.   Journal of Chemical Information and Modeling

Structure-Based Virtual Screening: From Classical to Artificial Intelligence

(2020) Eduardo Habib Bechelane Maia et al.   Frontiers in Chemistry

CHARMM-GUI supports the Amber force fields

(2020) Jumin Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Application of Fragment-Based Drug Discovery to Versatile Targets

(2020) Qingxin Li   Frontiers in Molecular Biosciences

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

(2020) Hugo Guterres et al.   Journal of Chemical Information and Modeling

Stalis : A Computational Method for Template-Based Ab Initio Ligand Design

(2019) Hui Sun Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems

(2019) Yifei Qi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ligand-Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

(2019) Hugo Guterres et al.   Journal of Chemical Theory and Computation

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

(2018) Hongyi Zhou et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

(2018) Jumin Lee et al.   Journal of Chemical Theory and Computation

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

(2017) Seonghoon Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

(2017) Antoine Daina et al.   Scientific Reports

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

(2016) Ignacio Soteras Gutiérrez et al.   BIOORGANIC & MEDICINAL CHEMISTRY

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design

(2016) Hui Sun Lee et al.   PROTEIN SCIENCE

Fragment-Based Drug Discovery and Molecular Docking in Drug Design

(2015) Tao Wang et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity

(2015) Ambrish Roy et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

NGL Viewer: a web application for molecular visualization

(2015) Alexander S. Rose et al.   NUCLEIC ACIDS RESEARCH

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

(2014) Evanthia Lionta et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems

(2013) Xi Cheng et al.   Journal of Chemical Information and Modeling

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

(2013) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design

(2012) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

(2012) Sunhwan Jo et al.   Journal of Chemical Information and Modeling

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

LigBuilder 2: A Practicalde NovoDrug Design Approach

(2011) Yaxia Yuan et al.   Journal of Chemical Information and Modeling

BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures

(2011) Hui Sun Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Open Babel: An open chemical toolbox

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

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

(2010) Pierre Baldi et al.   Journal of Chemical Information and Modeling

Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir

(2010) I. F. Sevrioukova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket

(2009) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity

(2009) Fabrice Moriaud et al.   Journal of Chemical Information and Modeling

Androgen receptor as a potential sign of prostate cancer metastasis

(2009) Marie-Hélène Lévesque et al.   PROSTATE

Synthesis and structure based optimization of novel Akt inhibitors

(2008) Blaise Lippa et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Characterization of local geometry of protein surfaces with the visibility criterion

(2007) Bin Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS