OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling

Can AlphaFold2 predict the impact of missense mutations on structure?

(2022) Gwen R. Buel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DLPacker : Deep learning for prediction of amino acid side chain conformations in proteins

(2022) Mikita Misiura et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding

(2021) Gang Xu et al.   BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

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

(2021) Minkyung Baek et al.   SCIENCE

OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors

(2021) Gang Xu et al.   BRIEFINGS IN BIOINFORMATICS

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks

(2020) Gang Xu et al.   BIOINFORMATICS

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

(2020) Raghav Shroff et al.   ACS Synthetic Biology

OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods

(2020) Gang Xu 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

Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I

(2019) Shrikant Pawar et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

OPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method

(2019) Gang Xu et al.   Journal of Chemical Theory and Computation

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks

(2018) Jack Hanson et al.   BIOINFORMATICS

OPUS-CSF: A C-atom-based scoring function for ranking protein structural models

(2017) Gang Xu et al.   PROTEIN SCIENCE

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

(2017) Jürgen Haas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts

(2016) Zhanglong Liu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease

(2014) Ayşegül Özen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

A fluorescent curcumin-based Zn(II)-complex reactivates mutant (R175H and R273H) p53 in cancer cells

(2013) Alessia Garufi et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Structural Effects of the L145Q, V157F, and R282W Cancer-Associated Mutations in the p53 DNA-Binding Core Domain

(2011) Sara Calhoun et al.   BIOCHEMISTRY

Fast and accurate prediction of protein side-chain conformations

(2011) Shide Liang et al.   BIOINFORMATICS

Finding better protein engineering strategies

(2009) Romas J Kazlauskas et al.   Nature Chemical Biology

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS