#ApplicationNote

PymolFold: A PyMOL Plugin for API-Driven Structure Prediction and Quality Assessment #JCIM Vol66 Issue2 #ApplicationNote

MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini #JCIM Vol66 Issue15 #ApplicationNote

ThermoSeek: An Integrated Web Resource for Sequence and Structural Analysis of Proteins from Thermophilic Species #JCIM Vol65 Issue12 #ApplicationNote

FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses #JCIM Vol64 Issue18 #ApplicationNote

ChemTorch: A Deep Learning Framework for Benchmarking and Developing Chemical Reaction Property Prediction Models #DeepLearning #JCIM Vol66 Issue5 #ApplicationNote

Surface Adsorption and Geometry Evaluator (SAGE): An Interactive Workflow Platform for Standardized Surface Adsorption Screening #JCIM Vol66 Issue16 #ApplicationNote

Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations @ries_benj @HighSpeedMode @davidlmobley @openfreeenergy #JCIM Vol64 Issue22 #ApplicationNote

EasyDock 1.3: An Automated Pipeline for Molecular Docking #JCIM Vol66 Issue15 #ApplicationNote

Peptide-Tools–Web Server for Calculating Physicochemical Properties of Peptides #JCIM Vol66 Issue1 #ApplicationNote

PP-MAPS: Dynamic Pharmacophore Signatures of Protein–Peptide Interfaces from Molecular Dynamics Trajectories #JCIM Vol66 Issue13 #ApplicationNote

Extending the Python RESP Framework for Extra Point Charge Fitting #JCIM Vol66 Issue16 #ApplicationNote

3DSTarPred: A Web Server for Target Prediction of Bioactive Small Molecules Based on 3D Shape Similarity #JCIM Vol64 Issue21 #ApplicationNote

DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host–Guest Complexation #Docking #JCIM Vol66 Issue4 #ApplicationNote

SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis #JCIM Vol65 Issue24 #ApplicationNote

MechaSuite: An Integrated Software for Chemical Reaction Mechanism Analysis and Microkinetic Modeling #JCIM Vol66 Issue10 #ApplicationNote

af3cli: Streamlining AlphaFold3 Input Preparation #AlphaFold #JCIM Vol65 Issue8 #ApplicationNote

MacGen: A Web Server for Structure-Based Macrocycle Design @xiaolinpan1 @chemphy123 #JCIM Vol64 Issue24 #ApplicationNote

ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation #ADMET @SPodlewska #JCIM Vol64 Issue5 #ApplicationNote

lmp2gro: A Python Tool for Converting LAMMPS Data Files into GROMACS Topologies #JCIM Vol66 Issue15 #ApplicationNote

PDBTools.jl: A Lightweight and High-Performance Julia Package for Molecular Structure File Handling and Analysis #JCIM Vol66 Issue11 #ApplicationNote