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Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

PLoS computational biology, 2015-12, Vol.11 (12), p.e1004580-e1004580

2015

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From complete cross-docking to partners identification and binding sites predictions

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009825-e1009825

2022

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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Proteins, structure, function, and bioinformatics, 2019-12, Vol.87 (12), p.1200-1221

2019

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Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import

PLoS genetics, 2023-08, Vol.19 (8), p.e1010848-e1010848

2023

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Explaining Conformational Diversity in Protein Families through Molecular Motions

Scientific data, 2024-07, Vol.11 (1), p.752-17, Article 752

2024

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Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007624-e1007624

2020

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Allosteric communication across the native and mutated KIT receptor tyrosine kinase

PLoS computational biology, 2012-08, Vol.8 (8), p.e1002661

2012

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Predicting substitutions to modulate disorder and stability in coiled-coils

BMC bioinformatics, 2020-12, Vol.21 (Suppl 19), p.573-573, Article 573

2020

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Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

Scientific reports, 2016-05, Vol.6 (1), p.26401-26401, Article 26401

2016

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Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

PLoS computational biology, 2013-12, Vol.9 (12), p.e1003369-e1003369

2013

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Mutation D816V alters the internal structure and dynamics of c-KIT receptor cytoplasmic region: implications for dimerization and activation mechanisms

PLoS computational biology, 2011-06, Vol.7 (6), p.e1002068-e1002068

2011

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Targeting Solute Carrier Transporters through Functional Mapping

Trends in pharmacological sciences (Regular ed.), 2021-01, Vol.42 (1), p.3-6

2021

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Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003749-e1003749

2014

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HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps

The journal of physical chemistry. B, 2021-03, Vol.125 (10), p.2577-2588

2021

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GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

Molecular biology and evolution, 2019-11, Vol.36 (11), p.2604-2619

2019

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Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (25), p.11277-11282

2010

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Differential effects of CSF-1R D802V and KIT D816V homologous mutations on receptor tertiary structure and allosteric communication

PloS one, 2014-05, Vol.9 (5), p.e97519-e97519

2014

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Protein social behavior makes a stronger signal for partner identification than surface geometry

Proteins, structure, function, and bioinformatics, 2017-01, Vol.85 (1), p.137-154

2017

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Meet-U: Educating through research immersion

PLoS computational biology, 2018-03, Vol.14 (3), p.e1005992-e1005992

2018

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ASES: visualizing evolutionary conservation of alternative splicing in proteins

Bioinformatics (Oxford, England), 2022-04, Vol.38 (9), p.2615-2616

2022

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Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?

Proteins, structure, function, and bioinformatics, 2021-12, Vol.89 (12), p.1770-1786

2021

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Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity

Structure (London), 2018-06, Vol.26 (6), p.905-915.e4

2018

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Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation

Bioinformatics (Oxford, England), 2023-06, Vol.39 (Supplement_1), p.i544-i552

2023

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Predicting Protein Functional Motions: an Old Recipe with a New Twist

Biophysical journal, 2020-05, Vol.118 (10), p.2513-2525

2020

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Building alternative splicing and evolution-aware sequence-structure maps for protein repeats

Journal of structural biology, 2023-09, Vol.215 (3), p.107997-107997, Article 107997

2023

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Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

From complete cross-docking to partners identification and binding sites predictions

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import

Explaining Conformational Diversity in Protein Families through Molecular Motions

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

Allosteric communication across the native and mutated KIT receptor tyrosine kinase

Predicting substitutions to modulate disorder and stability in coiled-coils

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

Mutation D816V alters the internal structure and dynamics of c-KIT receptor cytoplasmic region: implications for dimerization and activation mechanisms

Targeting Solute Carrier Transporters through Functional Mapping

Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity

HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps

GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor

Differential effects of CSF-1R D802V and KIT D816V homologous mutations on receptor tertiary structure and allosteric communication

Protein social behavior makes a stronger signal for partner identification than surface geometry

Meet-U: Educating through research immersion

ASES: visualizing evolutionary conservation of alternative splicing in proteins

Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?

Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity

Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation

Predicting Protein Functional Motions: an Old Recipe with a New Twist

Building alternative splicing and evolution-aware sequence-structure maps for protein repeats

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