Skolnick, Jeffrey

Scoring function for automated assessment of protein structure template quality

Zhang, Y., & Skolnick, J. (2004) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2,392

Topology fingerprint approach to the inverse protein folding problem

Godzik, A., Kolinski, A., & Skolnick, J. (1992) · Journal of Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 339

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

Brylinski, M., & Skolnick, J. (2008) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 333

The protein structure prediction problem could be solved using the current PDB library

Zhang, Y., & Skolnick, J. (2005) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 297

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Gao, M., Nakajima An, D., Parks, J. M., & Skolnick, J. (2022) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 252

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

Skolnick, J., Gao, M., Zhou, H., & Singh, S. (2021) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 251

On the origin and highly likely completeness of single-domain protein structures

Zhang, Y., Hubner, I. A., Arakaki, A. K., Shakhnovich, E., & Skolnick, J. (2006) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 197

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

Gao, M., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 139

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

Zhou, H., Gao, M., & Skolnick, J. (2015) · Scientific Reports

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 138

Insights into disease-associated mutations in the human proteome through protein structural analysis

Gao, M., Zhou, H., & Skolnick, J. (2015) · Structure

Genomics and Rare DiseasesProtein Structure and Dynamics

Cited by 113

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

Gao, M., & Skolnick, J. (2010) · Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 98

De novo and inverse folding predictions of protein structure and dynamics

Godzik, A., Kolinski, A., & Skolnick, J. (1993) · Journal of Computer-Aided Molecular Design

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 91

All-Atom Ab Initio Folding of a Diverse Set of Proteins

Yang, J. S., Chen, W. W., Skolnick, J., & Shakhnovich, E. I. (2007) · Structure

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 86

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

Chen, H., & Skolnick, J. (2008) · Biophysical Journal

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 68

DESTINI: A deep-learning approach to contact-driven protein structure prediction

Gao, M., Zhou, H., & Skolnick, J. (2019) · Scientific Reports

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 61

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Guo, Z., Liu, J., Skolnick, J., & Cheng, J. (2022) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 58

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Guo, Z., Liu, J., Skolnick, J., & Cheng, J. (2022) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 57

On the possible origin of protein homochirality, structure, and biochemical function

Skolnick, J., Zhou, H., & Gao, M. (2019) · Proceedings of the National Academy of Sciences

Origins and Evolution of LifeRNA and protein synthesis mechanisms

Cited by 45

New benchmark metrics for protein‐protein docking methods

Gao, M., & Skolnick, J. (2011) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 42

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

Zhou, H., Cao, H., & Skolnick, J. (2018) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 39

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

Zhou, H., Cao, H., Matyunina, L., Shelby, M., Cassels, L., McDonald, J. F., & Skolnick, J. (2020) · Molecular Pharmaceutics

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 39

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

Skolnick, J., Zhou, H., & Brylinski, M. (2012) · The Journal of Physical Chemistry B

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 35

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening

Zhou, H., Cao, H., & Skolnick, J. (2021) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 32

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

Tonddast-Navaei, S., & Skolnick, J. (2015) · The Journal of Chemical Physics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 31