AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

(2021) Tianqi Wu et al.   BMC BIOINFORMATICS

Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction

(2021) Chen Chen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening

(2021) Hongyi Zhou et al.   Journal of Chemical Information and Modeling

Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies

(2021) Jianzhong Chen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

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

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

(2021) Jian Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14

(2021) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2021) Minkyung Baek et al.   SCIENCE

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

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

MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action

(2020) Hongyi Zhou et al.   MOLECULAR PHARMACEUTICS

How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs

(2020) Mariona Torrens-Fontanals et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The AutoDock suite at 30

(2020) David S. Goodsell et al.   PROTEIN SCIENCE

Conformational states dynamically populated by a kinase determine its function

(2020) Tao Xie et al.   SCIENCE

Predicting binding sites from unbound versus bound protein structures

(2020) Jordan J. Clark et al.   Scientific Reports

RCSB Protein Data Bank 1D tools and services

(2020) Joan Segura et al.   BIOINFORMATICS

The role of local versus nonlocal physicochemical restraints in determining protein native structure

(2020) Jeffrey Skolnick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Defining a new nomenclature for the structures of active and inactive kinases

(2019) Vivek Modi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

(2019) Yang Li et al.   BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Basis of G Protein–Coupled Receptor Activation

(2018) William I. Weis et al.   Annual Review of Biochemistry

Cryptic binding sites on proteins: definition, detection, and druggability

(2018) Sandor Vajda et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

(2018) Hongyi Zhou et al.   Journal of Chemical Information and Modeling

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

(2015) Sirish Kaushik Lakkaraju et al.   Journal of Chemical Information and Modeling

Are protein-protein interfaces special regions on a protein’s surface?

(2015) Sam Tonddast-Navaei et al.   JOURNAL OF CHEMICAL PHYSICS

ChSeq: A database of chameleon sequences

(2015) Wenlin Li et al.   PROTEIN SCIENCE

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

(2015) Jianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comprehensive prediction of drug-protein interactions and side effects for the human proteome

(2015) Hongyi Zhou et al.   Scientific Reports

Protein Conformational Populations and Functionally Relevant Substates

(2013) Arvind Ramanathan et al.   ACCOUNTS OF CHEMICAL RESEARCH

Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures

(2012) Jeffrey Skolnick et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Template-based protein structure modeling using TASSERVMT

(2011) Hongyi Zhou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Recovering physical potentials from a model protein databank

(2010) J. W. Mullinax et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected

(2010) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the helix packing of globular proteins by self-correcting distance geometry

(2010) C.H. Mumenthaler et al.   PROTEIN SCIENCE

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS