Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins

Protein sequence design with a learned potential

(2022) Namrata Anand et al.   Nature Communications

MIB2: metal ion-binding site prediction and modeling server

(2022) Chih-Hao Lu et al.   BIOINFORMATICS

GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network

(2022) Sangwoo Park et al.   Journal of Chemical Information and Modeling

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Machine learning differentiates enzymatic and non-enzymatic metals in proteins

(2021) Ryan Feehan et al.   Nature Communications

Automatically Constructed Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins

(2021) Mingyuan Xu et al.   Frontiers in Chemistry

Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins

(2021) Zongfan Yang et al.   Journal of Chemical Information and Modeling

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

(2021) Nicolas Renaud et al.   Nature Communications

De novo metalloprotein design

(2021) Matthew J. Chalkley et al.   Nature Reviews Chemistry

Thermodynamics of Transition Metal Ion Binding to Proteins

(2020) Lin Frank Song et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites

(2020) Albert Kakkis et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning

(2020) Raghav Shroff et al.   ACS Synthetic Biology

BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization

(2020) José-Emilio Sánchez-Aparicio et al.   Journal of Chemical Information and Modeling

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

(2020) Bian Li et al.   PLoS Computational Biology

Prediction of Protein Metal Binding Sites Using Deep Neural Networks

(2019) İsmail Haberal et al.   Molecular Informatics

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

LigVoxel: Inpainting binding pockets using 3D-convolutional neural networks

(2018) Miha Skalic et al.   BIOINFORMATICS

Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein

(2018) Esra Bozkurt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fatty acyl recognition and transfer by an integral membraneS-acyltransferase

(2018) Mitra S. Rana et al.   SCIENCE

High Precision Protein Functional Site Detection Using 3D Convolutional Neural Networks

(2018) Wen Torng et al.   BIOINFORMATICS

Design of metalloproteins and novel protein folds using variational autoencoders

(2018) Joe G. Greener et al.   Scientific Reports

Evolution of a highly active and enantiospecific metalloenzyme from short peptides

(2018) Sabine Studer et al.   SCIENCE

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin

(2017) Akshay Sridhar et al.   PLoS One

Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

(2017) Shiran Barber-Zucker et al.   Scientific Reports

Recognizing metal and acid radical ion-binding sites by integratingab initiomodeling with template-based transferals

(2016) Xiuzhen Hu et al.   BIOINFORMATICS

MIB: Metal Ion-Binding Site Prediction and Docking Server

(2016) Yu-Feng Lin et al.   Journal of Chemical Information and Modeling

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Abiological catalysis by artificial haem proteins containing noble metals in place of iron

(2016) Hanna M. Key et al.   NATURE

Probing the minimal determinants of zinc binding with computational protein design

(2016) Sharon L. Guffy et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Dowser++, a new method of hydrating protein structures

(2016) A. Morozenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

(2015) Elizabeth Brunk et al.   CHEMICAL REVIEWS

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

Protein Design: Toward Functional Metalloenzymes

(2014) Fangting Yu et al.   CHEMICAL REVIEWS

Zinc Coordination Spheres in Protein Structures

(2013) Mikko Laitaoja et al.   INORGANIC CHEMISTRY

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

(2013) Heping Zheng et al.   Nature Protocols

Revisiting Zinc Coordination in Human Carbonic Anhydrase II

(2012) He Song et al.   INORGANIC CHEMISTRY

Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays

(2012) Jeffrey D. Brodin et al.   Nature Chemistry

Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method

(2012) Chih-Hao Lu et al.   PLoS One

Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

(2011) Bryan S. Der et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hydrolytic catalysis and structural stabilization in a designed metalloprotein

(2011) Melissa L. Zastrow et al.   Nature Chemistry

Metal-Directed Protein Self-Assembly

(2010) Eric N. Salgado et al.   ACCOUNTS OF CHEMICAL RESEARCH

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

(2010) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Metal ions in biological catalysis: from enzyme databases to general principles

(2008) Claudia Andreini et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

How do bacterial cells ensure that metalloproteins get the correct metal?

(2008) Kevin J. Waldron et al.   NATURE REVIEWS MICROBIOLOGY