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CAVER: a new tool to explore routes from protein clefts, pockets and cavities

BMC bioinformatics, 2006-06, Vol.7 (1), p.316-316, Article 316

2006

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Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Scientific reports, 2021-06, Vol.11 (1), p.12345-12345, Article 12345

2021

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Assessing the Performance of MM/PBSA, MM/GBSA, and QM–MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

The journal of physical chemistry. B, 2018-08, Vol.122 (34), p.8113-8121

2018

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Substrate-Assisted Catalytic Mechanism of O‑GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

Journal of the American Chemical Society, 2012-09, Vol.134 (37), p.15563-15571

2012

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Optimized SQE atomic charges for peptides accessible via a web application

Journal of cheminformatics, 2021-06, Vol.13 (1), p.45-45, Article 45

2021

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Correction to: Optimized SQE atomic charges for peptides accessible via a web application

Journal of cheminformatics, 2021-07, Vol.13 (1), p.52-52, Article 52

2021

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Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review

Molecules (Basel, Switzerland), 2020-06, Vol.25 (12), p.2835

2020

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MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Nucleic acids research, 2018-07, Vol.46 (W1), p.W368

2018

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LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

Nature methods, 2017-12, Vol.14 (12), p.1121

2017

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Structures and mechanisms of glycosyltransferases

Glycobiology (Oxford), 2006-02, Vol.16 (2), p.29R-37R

2006

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Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions

Journal of chemical theory and computation, 2018-01, Vol.14 (1), p.291-302

2018

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Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Journal of chemical theory and computation, 2014-03, Vol.10 (3), p.1326-1340

2014

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Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

Journal of chemical theory and computation, 2012-07, Vol.8 (7), p.2506-2520

2012

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The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Chemistry : a European journal, 2020-08, Vol.26 (47), p.10769-10780

2020

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MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Journal of cheminformatics, 2013-08, Vol.5 (1), p.39-39, Article 39

2013

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The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1

Physical chemistry chemical physics : PCCP, 2021-10, Vol.23 (41), p.2385-2386

2021

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Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study

Glycobiology (Oxford), 2021-09, Vol.31 (8), p.975-987

2021

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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Biochimie, 2014-10, Vol.105, p.22-35

2014

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BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

PLoS computational biology, 2020-10, Vol.16 (10), p.e1008247-e1008247

2020

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Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Journal of chemical theory and computation, 2015-07, Vol.11 (7), p.3333-3345

2015

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Exploring Reaction Pathways for O‑GlcNAc Transferase Catalysis. A String Method Study

The journal of physical chemistry. B, 2015-03, Vol.119 (12), p.4371-4381

2015

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MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels

Structure (London), 2007-11, Vol.15 (11), p.1357-1363

2007

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ChannelsDB: database of biomacromolecular tunnels and pores

Nucleic acids research, 2018-01, Vol.46 (D1), p.D399

2018

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Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

Journal of chemical theory and computation, 2009-09, Vol.5 (9), p.2514-2530

2009

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PDBe: improved findability of macromolecular structure data in the PDB

Nucleic acids research, 2020-01, Vol.48 (D1), p.D335

2020

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CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Assessing the Performance of MM/PBSA, MM/GBSA, and QM–MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

Substrate-Assisted Catalytic Mechanism of O‑GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

Optimized SQE atomic charges for peptides accessible via a web application

Correction to: Optimized SQE atomic charges for peptides accessible via a web application

Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

Structures and mechanisms of glycosyltransferases

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1

Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Exploring Reaction Pathways for O‑GlcNAc Transferase Catalysis. A String Method Study

MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels

ChannelsDB: database of biomacromolecular tunnels and pores

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

PDBe: improved findability of macromolecular structure data in the PDB

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