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CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Nucleic acids research, 2015-07, Vol.43 (W1), p.W419-W424

2015

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CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Nucleic acids research, 2018-07, Vol.46 (W1), p.W338-W343

2018

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Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

Nucleic acids research, 2019-07, Vol.47 (W1), p.W300-W307

2019

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Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

Methods (San Diego, Calif.), 2016-01, Vol.93, p.72-83

2016

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Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking

Molecules (Basel, Switzerland), 2021-05, Vol.26 (11), p.3293

2021

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Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations

International journal of molecular sciences, 2021-07, Vol.22 (14), p.7341

2021

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Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

Biophysical journal, 2008-02, Vol.94 (3), p.726-736

2008

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Computational reconstruction of atomistic protein structures from coarse-grained models

Computational and structural biotechnology journal, 2020-01, Vol.18, p.162-176

2020

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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

International journal of molecular sciences, 2018-11, Vol.19 (11), p.3496

2018

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Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

The Journal of chemical physics, 2018-06, Vol.148 (21), p.215106-215106

2018

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Characterization of protein-folding pathways by reduced-space modeling

Proceedings of the National Academy of Sciences - PNAS, 2007-07, Vol.104 (30), p.12330-12335

2007

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Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

International journal of molecular sciences, 2019-01, Vol.20 (3), p.606

2019

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Novel Tetrazole-Based Antimicrobial Agents Targeting Clinical Bacteria Strains: Exploring the Inhibition of Staphylococcus aureus DNA Topoisomerase IV and Gyrase

International journal of molecular sciences, 2021-12, Vol.23 (1), p.378

2021

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Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model

Journal of chemical information and modeling, 2016-11, Vol.56 (11), p.2207-2215

2016

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Menthol- and thymol-based ciprofloxacin derivatives against Mycobacterium tuberculosis: in vitro activity, lipophilicity, and computational studies

Scientific reports, 2023-09, Vol.13 (1), p.16328-16328, Article 16328

2023

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The Effect of Conjugation of Ciprofloxacin and Moxifloxacin with Fatty Acids on Their Antibacterial and Anticancer Activity

International journal of molecular sciences, 2022-06, Vol.23 (11), p.6261

2022

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Antibacterial and anti-biofilm activities of new fluoroquinolone derivatives coupled with nitrogen-based heterocycles

Biomedicine & pharmacotherapy, 2024-10, Vol.179, p.117439, Article 117439

2024

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A3DyDB: exploring structural aggregation propensities in the yeast proteome

Microbial cell factories, 2023-09, Vol.22 (1), p.1-186, Article 186

2023

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Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility

Molecular pharmaceutics, 2018-09, Vol.15 (9), p.3846-3859

2018

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Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

Journal of computational chemistry, 2007-07, Vol.28 (9), p.1593-1597

2007

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The Synergistic Effect of N2 and N7 Modifications on the Inhibitory Efficacy of mRNA Cap Analogues

Pharmaceuticals (Basel, Switzerland), 2024-05, Vol.17 (5), p.632

2024

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Design and Synthesis of Menthol and Thymol Derived Ciprofloxacin: Influence of Structural Modifications on the Antibacterial Activity and Anticancer Properties

International journal of molecular sciences, 2022-06, Vol.23 (12), p.6600

2022

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Synthetic Transition from Thiourea-Based Compounds to Tetrazole Derivatives: Structure and Biological Evaluation of Synthesized New N-(Furan-2-ylmethyl)-1H-tetrazol-5-amine Derivatives

Molecules (Basel, Switzerland), 2021-01, Vol.26 (2), p.323

2021

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Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53

Journal of advanced research, 2024-08, Vol.62, p.119-141

2024

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Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif

Biomedical engineering online, 2017-08, Vol.16 (Suppl 1), p.71-71, Article 71

2017

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CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility

Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking

Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations

Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

Computational reconstruction of atomistic protein structures from coarse-grained models

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Characterization of protein-folding pathways by reduced-space modeling

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

Novel Tetrazole-Based Antimicrobial Agents Targeting Clinical Bacteria Strains: Exploring the Inhibition of Staphylococcus aureus DNA Topoisomerase IV and Gyrase

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model

Menthol- and thymol-based ciprofloxacin derivatives against Mycobacterium tuberculosis: in vitro activity, lipophilicity, and computational studies

The Effect of Conjugation of Ciprofloxacin and Moxifloxacin with Fatty Acids on Their Antibacterial and Anticancer Activity

Antibacterial and anti-biofilm activities of new fluoroquinolone derivatives coupled with nitrogen-based heterocycles

A3DyDB: exploring structural aggregation propensities in the yeast proteome

Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility

Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

The Synergistic Effect of N2 and N7 Modifications on the Inhibitory Efficacy of mRNA Cap Analogues

Design and Synthesis of Menthol and Thymol Derived Ciprofloxacin: Influence of Structural Modifications on the Antibacterial Activity and Anticancer Properties

Synthetic Transition from Thiourea-Based Compounds to Tetrazole Derivatives: Structure and Biological Evaluation of Synthesized New N-(Furan-2-ylmethyl)-1H-tetrazol-5-amine Derivatives

Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53

Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif

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