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diff --git a/README.md b/README.md
@@ -23,8 +23,8 @@ The [CADD Vault](https://drugbud-suite.github.io/CADD_Vault/) includes resources
 - Machine Learning Applications in Drug Design
 - Fragment-Based Drug Design (FBDD)
 - Datasets for Drug Design
-Number of publications: 1116  
-Number of code repositories: 950  
+Number of publications: 1117  
+Number of code repositories: 951  
 Number of webserver links: 149  
 Number of webserver links: 123  
 

diff --git a/cadd_vault_data.xlsx b/cadd_vault_data.xlsx
diff --git a/docs/Cheminformatics/Chemical Format Translation.md b/docs/Cheminformatics/Chemical Format Translation.md
@@ -1,13 +1,13 @@
 ---
-icon: material/molecule
+icon: material/translate-variant
 ---
 
 - **Datagrok Bio**: Chemical format translation in Datagrok  
 	[![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://github.com/datagrok-ai/public/blob/74ca4a65d75f75f8bdadc84ecd399bc93d5a419c/packages/Bio/README.md#notations
 https://github.com/datagrok-ai/public/blob/4b6dfb43d88d3cb43ea587841a14e77cdea55b43/packages/Chem/README.md#molecular-format-conversion
 https://datagrok.ai/help/datagrok/solutions/domains/bio/oligo-toolkit#nucleotide-batch-conversion) 
 - **Meeko**: preparation of small molecules for AutoDock suite (.pdbqt format).  
-		[![Code](https://img.shields.io/github/stars/forlilab/Meeko?style=for-the-badge&logo=github)](https://github.com/forlilab/Meeko) [![Last Commit](https://img.shields.io/github/last-commit/forlilab/Meeko?style=for-the-badge&logo=github)](https://github.com/forlilab/Meeko) [![Publication](https://img.shields.io/badge/Publication-Citations:7-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1017/qrd.2022.18) 
+		[![Code](https://img.shields.io/github/stars/forlilab/Meeko?style=for-the-badge&logo=github)](https://github.com/forlilab/Meeko) [![Last Commit](https://img.shields.io/github/last-commit/forlilab/Meeko?style=for-the-badge&logo=github)](https://github.com/forlilab/Meeko) [![Publication](https://img.shields.io/badge/Publication-Citations:8-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1017/qrd.2022.18) 
 - **NAOMI**: consistent conversion of common chemical file formats (SDF, SMILES, MOL2)  
 	[![Publication](https://img.shields.io/badge/Publication-Citations:53-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/ci200324e) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.zbh.uni-hamburg.de/en/forschung/amd/software/naomi.html) 
 - **OpenBabel**: toolkit for drug discovery, file format etc (standalone)  

diff --git a/docs/Cheminformatics/Chemical Formulas.md b/docs/Cheminformatics/Chemical Formulas.md
@@ -1,5 +1,5 @@
 ---
-icon: material/molecule
+icon: material/format-subscript
 ---
 
 - **ChemFormula**: ON A SYSTEM OF INDEXING CHEMICAL LITERATURE; ADOPTED BY THE CLASSIFICATION DIVISION OF THE U. S. PATENT OFFICE.  

diff --git a/docs/Cheminformatics/Coordinates.md b/docs/Cheminformatics/Coordinates.md
@@ -1,5 +1,5 @@
 ---
-icon: material/molecule
+icon: material/axis-arrow
 ---
 
 - **chemcoord**: A python module for coordinates of molecules  

diff --git a/docs/Cheminformatics/General Tools.md b/docs/Cheminformatics/General Tools.md
@@ -10,3 +10,5 @@ icon: material/molecule
 	[![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.chemaxon.com/) 
 - **Datagrok Cheminformatics**: Cheminformatics functions in Datagrok  
 	[![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://datagrok.ai/help/datagrok/solutions/domains/chem/) 
+- **DataWarrior**: numerous tools (standalone).  
+	[![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](http://www.openmolecules.org/datawarrior/) 
diff --git a/docs/Cheminformatics/QM.md b/docs/Cheminformatics/QM.md
@@ -1,5 +1,5 @@
 ---
-icon: material/molecule
+icon: material/atom
 ---
 
 - **aqme**: AQME, or Automated Quantum Mechanical Environments, facilitates transparent and reproducible quantum chemistry workflows, supporting tasks like conformer generation, QM input file creation, and descriptor generation.  

diff --git a/docs/Cheminformatics/Reaction Tools.md b/docs/Cheminformatics/Reaction Tools.md
@@ -1,5 +1,5 @@
 ---
-icon: material/molecule
+icon: material/flask
 ---
 
 - **ChemPy**: ChemPy: A package useful for chemistry written in Python  

diff --git a/docs/Cheminformatics/Standalone.md b/docs/Cheminformatics/Standalone.md
diff --git a/docs/Cheminformatics/Workflow Managers.md b/docs/Cheminformatics/Workflow Managers.md
@@ -1,5 +1,5 @@
 ---
-icon: material/molecule
+icon: material/sitemap-outline
 ---
 
 - **maize**: a graph-based workflow manager for computational chemistry pipelines  

diff --git a/docs/Databases/Natural Products.md b/docs/Databases/Natural Products.md
@@ -15,7 +15,7 @@ icon: material/sprout
 - **Natural product subsets (DIFACQUIM)**: Natural product datasets (diverse with Python code to generate diversity) (dataset)  
 		[![Code](https://img.shields.io/github/stars/DIFACQUIM/Natural-products-subsets-generation?style=for-the-badge&logo=github)](https://github.com/DIFACQUIM/Natural-products-subsets-generation) [![Last Commit](https://img.shields.io/github/last-commit/DIFACQUIM/Natural-products-subsets-generation?style=for-the-badge&logo=github)](https://github.com/DIFACQUIM/Natural-products-subsets-generation) [![Publication](https://img.shields.io/badge/Publication-Citations:4-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1016/j.ailsci.2023.100066) 
 - **NPASS**: Natural product activity and species source database  
-	[![Publication](https://img.shields.io/badge/Publication-Citations:30-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkac1069) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://bidd.group/NPASS/) 
+	[![Publication](https://img.shields.io/badge/Publication-Citations:30-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gkac1069) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://bidd.group/NPASS/) 
 - **npatlas**: The Natural Products Atlas 2.0: A Database of Microbially-Derived Natural Products (online)  
 	[![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.npatlas.org/) 
 - **Nubbe**: a natural products database from the biodiversity of Brazil (online)  

diff --git a/docs/Databases/Protein-Ligand Interaction.md b/docs/Databases/Protein-Ligand Interaction.md
@@ -3,7 +3,7 @@ icon: material/tray-full
 ---
 
 - **BindingDB**: BindingDB contains data for over 1.2 million compounds and 9.2k targets, supporting research, education, and practice in drug discovery, pharmacology, and related fields.  
-	[![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gk) [![Link](https://img.shields.io/badge/Link-offline-red?style=for-the-badge&logo=xamarin&logoColor=red)](https://www.bindingdb.org/bind/index.jsp) 
+	[![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/nar/gk) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](https://www.bindingdb.org/bind/index.jsp) 
 - **BindingNet**: BindingNet is a dataset for analyzing protein-ligand interactions, containing modeled poses for compounds similar to the crystal ligands found in PDBbind, along with corresponding activities from ChEMBL.  
 		[![Code](https://img.shields.io/github/stars/hnlab/BindingNet?style=for-the-badge&logo=github)](https://github.com/hnlab/BindingNet) [![Last Commit](https://img.shields.io/github/last-commit/hnlab/BindingNet?style=for-the-badge&logo=github)](https://github.com/hnlab/BindingNet) [![Publication](https://img.shields.io/badge/Publication-Citations:2-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.3c01170) [![Link](https://img.shields.io/badge/Link-online-brightgreen?style=for-the-badge&logo=cachet&logoColor=65FF8F)](http://bindingnet.huanglab.org.cn/) 
 - **BioLip2**: BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions, aiming to serve the needs of ligand-protein docking, virtual ligand screening, and protein function annotation.  

diff --git a/docs/De Novo Generation/3D.md b/docs/De Novo Generation/3D.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/rotate-3d
 ---
 
 

diff --git a/docs/De Novo Generation/Active Learning.md b/docs/De Novo Generation/Active Learning.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/restore
 ---
 
 - **MF-LAL**: MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning  

diff --git a/docs/De Novo Generation/Bioisostere.md b/docs/De Novo Generation/Bioisostere.md
diff --git a/docs/De Novo Generation/Bioisosteres.md b/docs/De Novo Generation/Bioisosteres.md
@@ -2,6 +2,8 @@
 icon: material/approximately-equal
 ---
 
+- **ShEPhERD**: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design  
+		[![Code](https://img.shields.io/github/stars/coleygroup/shepherd?style=for-the-badge&logo=github)](https://github.com/coleygroup/shepherd) [![Last Commit](https://img.shields.io/github/last-commit/coleygroup/shepherd?style=for-the-badge&logo=github)](https://github.com/coleygroup/shepherd) [![Publication](https://img.shields.io/badge/Publication-Citations:0-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.48550/arXiv.2411.04130) 
 
 ## **Database Mining Approach**
 - **SwissBioisostere**: provide bioisosteres for a molecular fragment selected by a medicinal chemist  

diff --git a/docs/De Novo Generation/Diffusion.md b/docs/De Novo Generation/Diffusion.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/blur
 ---
 
 - **DrugDiff**: latent diffusion model — DrugDiff — paired with predictor guidance to generate novel compounds with a variety of desired molecular properties  

diff --git a/docs/De Novo Generation/Evolutionary.md b/docs/De Novo Generation/Evolutionary.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/sitemap-outline
 ---
 
 - **LEADD**: Lamarckian evolutionary algorithm for de novo drug design (standalone)  

diff --git a/docs/De Novo Generation/Flow Matching.md b/docs/De Novo Generation/Flow Matching.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/wave
 ---
 
 - **FlowMol**: Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation  

diff --git a/docs/De Novo Generation/Fragment-based.md b/docs/De Novo Generation/Fragment-based.md
@@ -1,5 +1,5 @@
 ---
-icon: material/sitemap-outline
+icon: material/arrange-bring-forward
 ---
 
 - **CRem**: open-source Python framework to generate chemical structures using a fragment-based approach  

diff --git a/docs/De Novo Generation/GAN.md b/docs/De Novo Generation/GAN.md
@@ -1,5 +1,5 @@
 ---
-icon: material/sitemap-outline
+icon: material/network-outline
 ---
 
 - **GAN-Drug-Generator**: Proposes a framework based on Feedback Generative Adversarial Network (GAN) for the generation and optimization of drug-like molecules, including a multiobjective optimization selection technique.  

diff --git a/docs/De Novo Generation/Monte Carlo Tree Seach.md b/docs/De Novo Generation/Monte Carlo Tree Seach.md
@@ -5,4 +5,4 @@ icon: material/arrow-decision-outline
 - **SyntheMol**: SyntheMol is a generative AI method for designing structurally novel and diverse drug candidates with predicted bioactivity that are easy to synthesize.  
 		[![Code](https://img.shields.io/github/stars/swansonk14/SyntheMol?style=for-the-badge&logo=github)](https://github.com/swansonk14/SyntheMol) [![Last Commit](https://img.shields.io/github/last-commit/swansonk14/SyntheMol?style=for-the-badge&logo=github)](https://github.com/swansonk14/SyntheMol) [![Publication](https://img.shields.io/badge/Publication-Citations:25-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1038/s42256-024-00809-7) 
 - **VGAE-MCTS**: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search (generative chemistry combining deep learning and reinforcement learning based on a molecular graph representation) (standalone).  
-		[![Code](https://img.shields.io/github/stars/clinfo/VGAE-MCTS?style=for-the-badge&logo=github)](https://github.com/clinfo/VGAE-MCTS) [![Last Commit](https://img.shields.io/github/last-commit/clinfo/VGAE-MCTS?style=for-the-badge&logo=github)](https://github.com/clinfo/VGAE-MCTS) [![Publication](https://img.shields.io/badge/Publication-Citations:3-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.3c01220) 
+		[![Code](https://img.shields.io/github/stars/clinfo/VGAE-MCTS?style=for-the-badge&logo=github)](https://github.com/clinfo/VGAE-MCTS) [![Last Commit](https://img.shields.io/github/last-commit/clinfo/VGAE-MCTS?style=for-the-badge&logo=github)](https://github.com/clinfo/VGAE-MCTS) [![Publication](https://img.shields.io/badge/Publication-Citations:4-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.3c01220) 
diff --git a/docs/De Novo Generation/Multi-modal.md b/docs/De Novo Generation/Multi-modal.md
@@ -9,4 +9,4 @@ icon: material/bookmark-multiple
 - **DrugEx**: Library for de novo drug design using RNNs, Transformers within a multi-objective reinforcement learning framework  
 		[![Code](https://img.shields.io/github/stars/CDDLeiden/DrugEx?style=for-the-badge&logo=github)](https://github.com/CDDLeiden/DrugEx) [![Last Commit](https://img.shields.io/github/last-commit/CDDLeiden/DrugEx?style=for-the-badge&logo=github)](https://github.com/CDDLeiden/DrugEx) [![Publication](https://img.shields.io/badge/Publication-Citations:9-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1021/acs.jcim.3c00434) 
 - **Sc2Mol**: A scaffold-based two-step molecule generator that combines variational autoencoders with transformers to generate molecules, supporting batch random generation for efficiency.  
-		[![Code](https://img.shields.io/github/stars/zhiruiliao/Sc2Mol?style=for-the-badge&logo=github)](https://github.com/zhiruiliao/Sc2Mol) [![Last Commit](https://img.shields.io/github/last-commit/zhiruiliao/Sc2Mol?style=for-the-badge&logo=github)](https://github.com/zhiruiliao/Sc2Mol) [![Publication](https://img.shields.io/badge/Publication-Citations:6-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/bioinformatics/btac814) 
+		[![Code](https://img.shields.io/github/stars/zhiruiliao/Sc2Mol?style=for-the-badge&logo=github)](https://github.com/zhiruiliao/Sc2Mol) [![Last Commit](https://img.shields.io/github/last-commit/zhiruiliao/Sc2Mol?style=for-the-badge&logo=github)](https://github.com/zhiruiliao/Sc2Mol) [![Publication](https://img.shields.io/badge/Publication-Citations:8-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1093/bioinformatics/btac814) 
diff --git a/docs/De Novo Generation/Multiobjective.md b/docs/De Novo Generation/Multiobjective.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/chart-multiple
 ---
 
 - **MOMO**: multiobjective molecule optimization framework (MOMO)  

diff --git a/docs/De Novo Generation/Other.md b/docs/De Novo Generation/Other.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/dots-horizontal
 ---
 
 - **MACAW**: an accessible tool for molecular embedding and inverse molecular design (generative chemistry) (standalone)  

diff --git a/docs/De Novo Generation/Pharmacophore.md b/docs/De Novo Generation/Pharmacophore.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/dots-hexagon
 ---
 
 - **DEVELOP**: Implements Deep Generative Design with 3D Pharmacophoric Constraints for molecular design, focusing on linker design and scaffold elaboration using a combination of variational autoencoders and 3D pharmacophore modeling.  

diff --git a/docs/De Novo Generation/Polypharmacology.md b/docs/De Novo Generation/Polypharmacology.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/vector-polygon
 ---
 
 - **POLYGON**: POLYGON attempts to optimize the chemical space for multiple protein target domains  

diff --git a/docs/De Novo Generation/Reinforcement Learning.md b/docs/De Novo Generation/Reinforcement Learning.md
@@ -1,5 +1,5 @@
 ---
-icon: material/new-box
+icon: material/read
 ---
 
 - **Acegen-Open**: TorchRL-based toolkit for reinforcement learning in generative chemistry  
@@ -15,7 +15,7 @@ icon: material/new-box
 - **ReLeaSE**: Utilizes deep reinforcement learning for de novo drug design.  
 		[![Code](https://img.shields.io/github/stars/isayev/ReLeaSE?style=for-the-badge&logo=github)](https://github.com/isayev/ReLeaSE) [![Last Commit](https://img.shields.io/github/last-commit/isayev/ReLeaSE?style=for-the-badge&logo=github)](https://github.com/isayev/ReLeaSE) [![Publication](https://img.shields.io/badge/Publication-Citations:816-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1126/sciadv.aap7885) 
 - **RL-GraphInvent**: An extension using reinforcement learning for targeted molecular generation.  
-		[![Code](https://img.shields.io/github/stars/olsson-group/RL-GraphINVENT?style=for-the-badge&logo=github)](https://github.com/olsson-group/RL-GraphINVENT) [![Last Commit](https://img.shields.io/github/last-commit/olsson-group/RL-GraphINVENT?style=for-the-badge&logo=github)](https://github.com/olsson-group/RL-GraphINVENT) [![Publication](https://img.shields.io/badge/Publication-Citations:87-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1088/2632-2153/abcf91) 
+		[![Code](https://img.shields.io/github/stars/olsson-group/RL-GraphINVENT?style=for-the-badge&logo=github)](https://github.com/olsson-group/RL-GraphINVENT) [![Last Commit](https://img.shields.io/github/last-commit/olsson-group/RL-GraphINVENT?style=for-the-badge&logo=github)](https://github.com/olsson-group/RL-GraphINVENT) [![Publication](https://img.shields.io/badge/Publication-Citations:86-blue?style=for-the-badge&logo=bookstack)](https://doi.org/10.1088/2632-2153/abcf91) 
 
 ## **Human-in-the-loop**
 - **REINVENT-HITL**: Focuses on human-in-the-loop assisted de novo molecular design, leveraging reinforcement learning for optimizing molecules based on human feedback.