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A knowledge-based approach for predicting gene-disease associations

Bioinformatics (Oxford, England), 2016-09, Vol.32 (18), p.2831-2838

2016

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A comprehensive survey of small-molecule binding pockets in proteins

PLoS computational biology, 2013-10, Vol.9 (10), p.e1003302

2013

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APoc: large-scale identification of similar protein pockets

Bioinformatics, 2013-03, Vol.29 (5), p.597-604

2013

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Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

Proceedings of the National Academy of Sciences - PNAS, 2010-10, Vol.107 (43), p.18457-18462

2010

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Fast procedure for reconstruction of full-atom protein models from reduced representations

Journal of computational chemistry, 2008-07, Vol.29 (9), p.1460-1465

2008

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

Nature communications, 2022-11, Vol.13 (1), p.6963-6963, Article 6963

2022

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

Proceedings of the National Academy of Sciences - PNAS, 2008-01, Vol.105 (1), p.129-134

2008

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AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Nature communications, 2022-04, Vol.13 (1), p.1744-13, Article 1744

2022

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Ab initio modeling of small proteins by iterative TASSER simulations

BMC biology, 2007-05, Vol.5 (1), p.17-17, Article 17

2007

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

Proceedings of the National Academy of Sciences - PNAS, 2019-12, Vol.116 (52), p.26571-26579

2019

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

Scientific reports, 2015-06, Vol.5 (1), p.11090-11090, Article 11090

2015

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distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

Proceedings of the National Academy of Sciences - PNAS, 2012-03, Vol.109 (10), p.3784-3789

2012

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Effects of confinement on models of intracellular macromolecular dynamics

Proceedings of the National Academy of Sciences - PNAS, 2015-12, Vol.112 (48), p.14846-14851

2015

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

BMC bioinformatics, 2008-12, Vol.9 (1), p.531-531, Article 531

2008

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In quest of an empirical potential for protein structure prediction

Current opinion in structural biology, 2006-04, Vol.16 (2), p.166-171

Skolnick, Jeffrey

2006

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Interplay of physics and evolution in the likely origin of protein biochemical function

Proceedings of the National Academy of Sciences - PNAS, 2013-06, Vol.110 (23), p.9344-9349

2013

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DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

Nucleic acids research, 2008-07, Vol.36 (12), p.3978-3992

2008

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Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models

PLoS computational biology, 2014-12, Vol.10 (12), p.e1003990-e1003990

2014

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

Proteins, structure, function, and bioinformatics, 2011-03, Vol.79 (3), p.735-751

2011

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PHEVIR: an artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases

Scientific reports, 2022-12, Vol.12 (1), p.20889-14, Article 20889

2022

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

Proceedings of the National Academy of Sciences - PNAS, 2010-12, Vol.107 (52), p.22517-22522

2010

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Assessment of programs for ligand binding affinity prediction

Journal of computational chemistry, 2008-06, Vol.29 (8), p.1316-1331

2008

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ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations

PloS one, 2018-05, Vol.13 (5), p.e0196849-e0196849

2018

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SPICKER: A clustering approach to identify near-native protein folds

Journal of computational chemistry, 2004-04, Vol.25 (6), p.865-871

2004

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Automated Structure Prediction of Weakly Homologous Proteins on a Genomic Scale

Proceedings of the National Academy of Sciences - PNAS, 2004-05, Vol.101 (20), p.7594-7599

2004

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A knowledge-based approach for predicting gene-disease associations

A comprehensive survey of small-molecule binding pockets in proteins

APoc: large-scale identification of similar protein pockets

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

Fast procedure for reconstruction of full-atom protein models from reduced representations

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

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

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Ab initio modeling of small proteins by iterative TASSER simulations

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

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

distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

Effects of confinement on models of intracellular macromolecular dynamics

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

In quest of an empirical potential for protein structure prediction

Interplay of physics and evolution in the likely origin of protein biochemical function

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models

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

PHEVIR: an artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases

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

Assessment of programs for ligand binding affinity prediction

ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations

SPICKER: A clustering approach to identify near-native protein folds

Automated Structure Prediction of Weakly Homologous Proteins on a Genomic Scale

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