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JCIM & JCTC Journals@JCIM_JCTC
Jun 6
MOFSynth-ADV: An Open-Source Engine for Synthesizability Evaluation of Metal–Organic Frameworks pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

MOFSynth-ADV: An Open-Source Engine for Synthesizability Evaluation of Metal–Organic Frameworks

We present MOFSynth-ADV, an advanced iteration of the MOFSynth tool designed to evaluate the synthetic feasibility of Metal–Organic Frameworks (MOFs). By integrating the Atomic Simulation Environment...

pubs.acs.org
4
7
644
JCIM & JCTC Journals@JCIM_JCTC
Jun 6
SLIDE: Quantifying Transmembrane Protein Interface Specificity through Persistence Score and Friction Energy pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

SLIDE: Quantifying Transmembrane Protein Interface Specificity through Persistence Score and...

Molecular dynamics simulations of transmembrane protein interfaces generate trajectories in which residue–residue contacts are continuously formed, broken, and reorganized. Existing analyses quantify...

pubs.acs.org
1
5
498
JCIM & JCTC Journals@JCIM_JCTC
Jun 6
SuAVE-Scatter: A Module for Integrating Simulations and SAXS/SANS Analyses pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

SuAVE-Scatter: A Module for Integrating Simulations and SAXS/SANS Analyses

We present two new functionalities implemented in the SuAVE software package for computing small-angle X-ray and neutron scattering (SAXS/SANS) profiles from molecular simulation data. The first...

pubs.acs.org
4
11
528
JCIM & JCTC Journals@JCIM_JCTC
Jun 6
Ensemble Analyzer: An Open-Source Python Framework for Automated Conformer Ensemble Refinement pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

Ensemble Analyzer: An Open-Source Python Framework for Automated Conformer Ensemble Refinement

Accurate prediction of molecular properties requires the refinement of the full conformational ensemble at high levels of theory, which remains computationally demanding. Existing workflows typically...

pubs.acs.org
6
33
1,220
JCIM & JCTC Journals@JCIM_JCTC
Jun 5
DRHIN: An Integrated and Interactive Web Server for Drug Repositioning pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

DRHIN: An Integrated and Interactive Web Server for Drug Repositioning

Drug repositioning (DR) identifies new therapeutic uses for approved drugs, reducing development burdens and offering safer treatment options for patients. While high-throughput technologies generate...

pubs.acs.org
1
6
453
JCIM & JCTC Journals@JCIM_JCTC
Jun 5
MolCrysKit: A Topology-Aware Toolkit for Bridging Experimental Molecular-Crystal Structures and Simulation-Ready Modeling pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

MolCrysKit: A Topology-Aware Toolkit for Bridging Experimental Molecular-Crystal Structures and...

Modeling molecular crystals requires addressing two main challenges: (i) maintaining the integrity of chemically bonded molecular units during structural operations and (ii) translating experimental...

pubs.acs.org
1
17
701
JCIM & JCTC Journals@JCIM_JCTC
Jun 5
Scalingk-Means for Multi-Million Frames: A Stratified NANI Approach for Large-Scale MD Simulations #MolecularDynamics pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ApplicationNote

Scaling k-Means for Multi-Million Frames: A Stratified NANI Approach for Large-Scale MD Simulations

We present improved k-means clustering initialization strategies for molecular dynamics (MD) simulations, implemented as part of the N-ary Natural Initiation (NANI) method. Two new deterministic...

pubs.acs.org
2
9
715
JCIM & JCTC Journals@JCIM_JCTC
Apr 28
AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue7 #ApplicationNote

AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline

AutoPocket2CREST is an automated workflow for preparing protein–ligand binding pockets for CREST conformational sampling. Starting from protein and ligand structures, the method identifies the...

pubs.acs.org
2
20
1,039
JCIM & JCTC Journals@JCIM_JCTC
Apr 28
AI-MedCraft: A Strategy-Driven AI Platform for Multi-Objective Molecular Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue7 #ApplicationNote

AI-MedCraft: A Strategy-Driven AI Platform for Multi-Objective Molecular Design

Small-molecule drug discovery requires balancing potency, selectivity, solubility, safety, and synthetic feasibility, among other interdependent properties. Yet most computational workflows address...

pubs.acs.org
21
892
JCIM & JCTC Journals@JCIM_JCTC
Apr 28
CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs #Docking pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue7 #ApplicationNote

CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs

Molecular docking aims to identify a biologically relevant binding pose of a ligand in the active site of a receptor. Reliable preparation of docking systems remains a key bottleneck in structure-b...

pubs.acs.org
14
39
1,893
JCIM & JCTC Journals@JCIM_JCTC
Apr 27
Integration of DOPtools and CADS in a Web-Based User Interface for Structural Descriptor Calculation, Model Optimization, and Prediction pubs.acs.org/doi/10.1021/acs… @ICReDDconnect @HokkaidoUni #JCIM Vol66 Issue7 #ApplicationNote

Integration of DOPtools and CADS in a Web-Based User Interface for Structural Descriptor Calculat...

Quantitative structure–property relationship (QSPR) modeling often requires navigating fragmented tools for descriptor calculation and model optimization. We present a major evolution of the CADS...

pubs.acs.org
1
11
926
JCIM & JCTC Journals@JCIM_JCTC
Apr 27
MXtalTools: A Toolkit for Machine Learning on Molecular Crystals #MachineLearning pubs.acs.org/doi/10.1021/acs… @kilgour_michael @GroupTuckerman #JCIM Vol66 Issue7 #ApplicationNote

MXtalTools: A Toolkit for Machine Learning on Molecular Crystals

We present MXtalTools, a flexible Python package for the data-driven modeling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several...

pubs.acs.org
2
15
647
JCIM & JCTC Journals@JCIM_JCTC
Apr 16
CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and Simulations #MolecularDynamics #MachineLearning pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue6 #ApplicationNote

CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and...

Recent advances in machine learning (ML) have enabled new developments in molecular dynamics simulation. Neural network potentials (NNPs) trained on quantum mechanical (QM) data provide highly...

pubs.acs.org
13
38
1,822
JCIM & JCTC Journals@JCIM_JCTC
Apr 15
plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output #MolecularDynamics #GROMACS pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue6 #ApplicationNote

plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output

Molecular simulation tools, such as GROMACS, are used routinely to produce time series of energies and other observables. To turn these data into publication-quality figures, a user can either use a...

pubs.acs.org
11
43
2,073
JCIM & JCTC Journals@JCIM_JCTC
Apr 2
Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL Data #DeepLearning pubs.acs.org/doi/10.1021/acs… @MaedehDarsaraee @jrjrjlr @reymondgroup #JCIM Vol66 Issue5 #ApplicationNote

Polypharmacology Browser PPB3: A Web-Based Deep Learning Tool for Target Prediction Using ChEMBL...

Drug-like molecules often interact with multiple biological targets. Assessing this polypharmacology is essential for drug development. Here, we trained deep neural networks to associate bioactive...

pubs.acs.org
4
12
536
JCIM & JCTC Journals@JCIM_JCTC
Apr 2
MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations #MolecularDynamics pubs.acs.org/doi/10.1021/acs… @G_Rossetti_ #JCIM Vol66 Issue5 #ApplicationNote

MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC...

Force matching (FM) algorithms develop force fields to dramatically extend the time scales of quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Here, we present...

pubs.acs.org
2
13
686
JCIM & JCTC Journals@JCIM_JCTC
Apr 2
MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue5 #ApplicationNote

MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation

High-quality molecular data sets are vital for reliable Quantitative Structure–Activity Relationship (QSAR) modeling and drug discovery. However, many molecular databases contain inaccuracies, such...

pubs.acs.org
2
13
654
JCIM & JCTC Journals@JCIM_JCTC
Apr 1
MDIntrinsicDimension: Dimensionality-Based Analysis of Collective Motions in Macromolecules from Molecular Dynamics Trajectories #MolecularDynamics pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue5 #ApplicationNote

MDIntrinsicDimension: Dimensionality-Based Analysis of Collective Motions in Macromolecules from...

Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such...

pubs.acs.org
6
27
979
JCIM & JCTC Journals@JCIM_JCTC
Apr 1
ChemTorch: A Deep Learning Framework for Benchmarking and Developing Chemical Reaction Property Prediction Models #DeepLearning pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue5 #ApplicationNote

ChemTorch: A Deep Learning Framework for Benchmarking and Developing Chemical Reaction Property...

Modeling of chemical reactions is essential for understanding kinetic mechanisms and predicting possible outcomes of reacting systems. Quantum mechanical calculations are accurate but often prohibi...

pubs.acs.org
5
37
1,013
JCIM & JCTC Journals@JCIM_JCTC
Apr 1
MolVE: An Open-Source Web Platform for Visualizing and Evaluating AI-Designed Molecules to Aid in Prioritization pubs.acs.org/doi/10.1021/acs… @DavideRigoni #JCIM Vol66 Issue5 #ApplicationNote

MolVE: An Open-Source Web Platform for Visualizing and Evaluating AI-Designed Molecules to Aid in...

Advances in artificial intelligence and deep generative models have enabled the rapid generation of novel molecular structures for advanced material science and drug discovery. However, the effective...

pubs.acs.org
3
10
881
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