List of works - Michal Brylinski

A graph-based approach to construct target-focused libraries for virtual screening

scientific article (publication date: 2016)

A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design.

scientific article

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

scholarly article

Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors

scientific article published on 5 March 2015

Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks

scientific article

An integrated network representation of multiple cancer-specific data for graph-based machine learning

scientific article published on 29 April 2022

Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions

scientific article

Assessing the similarity of ligand binding conformations with the Contact Mode Score

scientific article published on 6 September 2016

Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag.

scientific article

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

scientific article (publication date: 2015)

Comparative assessment of strategies to identify similar ligand-binding pockets in proteins

scientific article

Comparison of structure-based and threading-based approaches to protein functional annotation

scientific article published on January 2010

Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening ⬇️

scientific article published on October 25, 2010

Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries.

scientific article

Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family

scientific article published on 07 November 2007

Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach ⬇️

scientific article published on November 8, 2010

Cysteines and N-glycosylation Sites Conserved Among all Alphaherpesviruses Regulate Membrane Fusion in Herpes Simplex Virus Type 1 Infection

scientific article

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

scientific article published on 04 February 2019

Deletion of a Predicted β-Sheet Domain within the Amino Terminus of Herpes Simplex Virus Glycoprotein K Conserved among Alphaherpesviruses Prevents Virus Entry into Neuronal Axons

scientific article published on 9 December 2015

Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics.

scientific article

Early-stage folding in proteins (in silico) sequence-to-structure relation

scientific article

Elucidating the druggability of the human proteome with eFindSite

scientific article published on 19 March 2019

Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling.

scientific article

FINDSITE: a combined evolution/structure-based approach to protein function prediction

scientific article published on 26 March 2009

FINDSITE: a threading-based approach to ligand homology modeling

scientific article

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

scientific article published on December 6, 2010

Further evidence for the likely completeness of the library of solved single domain protein structures

scientific article

Gauss-function-Based model of hydrophobicity density in proteins

scientific article published on 01 January 2006

GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field

scientific article published on 6 August 2015

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

scientific article

Herpes Simplex Virus 1 UL37 Protein Tyrosine Residues Conserved among All Alphaherpesviruses Are Required for Interactions with Glycoprotein K, Cytoplasmic Virion Envelopment, and Infectious Virus Production.

scientific article

Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs

scientific article published on 12 October 2019

Hydrophobic collapse in (in silico) protein folding

scientific article

Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

scientific article published on 10 October 2019

Is the protein folding an aim-oriented process? Human haemoglobin as example

scientific article published on 01 January 2007

Large-scale computational drug repositioning to find treatments for rare diseases

scientific article

Ligation site in proteins recognized in silico.

scientific article

Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning.

scientific article published on January 2017

Localization of ligand binding site in proteins identified in silico.

scientific article published on 30 March 2007

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction

scientific article

PDID: database of molecular-level putative protein-drug interactions in the structural human proteome

scientific article

PSiFR: an integrated resource for prediction of protein structure and function.

scientific article

Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

scientific article published on 23 November 2015

Predicting protein interface residues using easily accessible on-line resources.

scientific article published on 21 March 2015

Prediction of functional sites based on the fuzzy oil drop model

scientific article

Prediction of ligand binding site and functionally important residues based on fuzzy-oil-drop model

scientific article published on 12 April 2007

Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning.

scientific article published in January 2015

Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

scientific article

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

scientific article published on July 2008

Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected.

scientific article published on 14 December 2009

SPI--structure predictability index for protein sequences.

scientific article

Sequence-structure-function relation characterized in silico

scientific article published on 01 October 2006

Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: biochemical and molecular modeling study

scientific article published on 16 May 2006

Structure-Based Drug Discovery Accelerated by Many-Core Devices

scientific article

SynerGNet: A Graph Neural Network Model to Predict Anticancer Drug Synergy

scientific article published in 2024

Template-based identification of protein-protein interfaces using eFindSitePPI.

scientific article published on 30 July 2015

The continuity of protein structure space is an intrinsic property of proteins

scientific article

The utility of artificially evolved sequences in protein threading and fold recognition

scientific article

The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement

scientific article

Unleashing the power of meta-threading for evolution/structure-based function inference of proteins

scientific article

Use of Protein Cross-Linking and Radiolytic Labeling To Elucidate the Structure of PsbO within Higher-Plant Photosystem II.

scientific article

Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II.

scientific article

What is the relationship between the global structures of apo and holo proteins?

scientific article

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function ⬇️

scientific article published on June 8, 2011

eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models

scientific article published on 12 February 2014

eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.

scientific article published in June 2013

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models

scientific article (publication date: September 2014)

eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database

eRepo-ORP: Exploring the Opportunity Space to Combat Orphan Diseases with Existing Drugs

scientific article published on 10 December 2017

eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures

scientific article

eToxPred: a machine learning-based approach to estimate the toxicity of drug candidates

article

eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

scientific article

List of works by Michal Brylinski

A graph-based approach to construct target-focused libraries for virtual screening

A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design.

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

Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors

Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks

An integrated network representation of multiple cancer-specific data for graph-based machine learning

Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions

Assessing the similarity of ligand binding conformations with the Contact Mode Score

Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag.

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

Comparative assessment of strategies to identify similar ligand-binding pockets in proteins

Comparison of structure-based and threading-based approaches to protein functional annotation

Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening ⬇️

Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries.

Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family

Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach ⬇️

Cysteines and N-glycosylation Sites Conserved Among all Alphaherpesviruses Regulate Membrane Fusion in Herpes Simplex Virus Type 1 Infection

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

Deletion of a Predicted β-Sheet Domain within the Amino Terminus of Herpes Simplex Virus Glycoprotein K Conserved among Alphaherpesviruses Prevents Virus Entry into Neuronal Axons

Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics.

Early-stage folding in proteins (in silico) sequence-to-structure relation

Elucidating the druggability of the human proteome with eFindSite

Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling.

FINDSITE: a combined evolution/structure-based approach to protein function prediction

FINDSITE: a threading-based approach to ligand homology modeling

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

Further evidence for the likely completeness of the library of solved single domain protein structures

Gauss-function-Based model of hydrophobicity density in proteins

GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Herpes Simplex Virus 1 UL37 Protein Tyrosine Residues Conserved among All Alphaherpesviruses Are Required for Interactions with Glycoprotein K, Cytoplasmic Virion Envelopment, and Infectious Virus Production.

Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs

Hydrophobic collapse in (in silico) protein folding

Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

Is the protein folding an aim-oriented process? Human haemoglobin as example

Large-scale computational drug repositioning to find treatments for rare diseases

Ligation site in proteins recognized in silico.

Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning.

Localization of ligand binding site in proteins identified in silico.

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction

PDID: database of molecular-level putative protein-drug interactions in the structural human proteome

PSiFR: an integrated resource for prediction of protein structure and function.

Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

Predicting protein interface residues using easily accessible on-line resources.

Prediction of functional sites based on the fuzzy oil drop model

Prediction of ligand binding site and functionally important residues based on fuzzy-oil-drop model

Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning.

Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected.

SPI--structure predictability index for protein sequences.

Sequence-structure-function relation characterized in silico

Stereoselectivity of 8-OH-DPAT toward the serotonin 5-HT1A receptor: biochemical and molecular modeling study

Structure-Based Drug Discovery Accelerated by Many-Core Devices

SynerGNet: A Graph Neural Network Model to Predict Anticancer Drug Synergy

Template-based identification of protein-protein interfaces using eFindSitePPI.

The continuity of protein structure space is an intrinsic property of proteins

The utility of artificially evolved sequences in protein threading and fold recognition

The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement

Unleashing the power of meta-threading for evolution/structure-based function inference of proteins

Use of Protein Cross-Linking and Radiolytic Labeling To Elucidate the Structure of PsbO within Higher-Plant Photosystem II.

Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II.

What is the relationship between the global structures of apo and holo proteins?

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function ⬇️

eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models

eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models

eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database

eRepo-ORP: Exploring the Opportunity Space to Combat Orphan Diseases with Existing Drugs

eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures

eToxPred: a machine learning-based approach to estimate the toxicity of drug candidates

eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.