Personal information

Biophysics, Proteins, Topology, Knots, Links, Molecular dynamics, Nucleotide sugars, Deep Learning, ChemInformatics
Poland

Activities

Employment (4)

Cardinal Stefan Wyszyński University in Warsaw: Warsaw, PL

2020-10-20 to present | Adiunkt (Faculty of Mathematics and Natural Sciences)
Employment
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Molecule.One: Warsaw, PL

2020-12-20 to 2023-03-31 | Computational Chemist (AI)
Employment
Source: Self-asserted source
Pawel Dabrowski-Tumanski

University of Warsaw: Warsaw, PL

2019-10 to 2020-10-13 | Adiunkt (Centre of New Technologies)
Employment
Source: Self-asserted source
Pawel Dabrowski-Tumanski

University of Lausanne: Lausanne, CH

2015-08-01 to 2015-09-10 | External Scientific Collaborator (Center for Integrative Genomics)
Employment
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Education and qualifications (4)

University of Warsaw: Warsaw, PL

2014-10-01 to 2019-09-24 | PhD (Faculty of Chemistry)
Education
Source: Self-asserted source
Pawel Dabrowski-Tumanski

University of Warsaw: Warsaw, PL

2011-10-01 to 2013-11-13 | MSc (Faculty of Chemistry)
Education
Source: Self-asserted source
Pawel Dabrowski-Tumanski

University of Warsaw: Warsaw, PL

2008-10-01 to 2012-09-28 | BSc (Faculty of Mathematics)
Education
Source: Self-asserted source
Pawel Dabrowski-Tumanski

University of Warsaw: Warsaw, PL

2008-10-01 to 2011-06-30 | BSc (Faculty of Chemistry)
Education
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Funding (3)

Study on methodology to find macrocyclic links in proteins

2016-07 to 2017-06 | Grant
University of Warsaw, Faculty of Chemistry (Warsaw, PL)
GRANT_NUMBER:

120000-501/86-DSM-112 700

Source: Self-asserted source
Pawel Dabrowski-Tumanski

Characterization of the structure/function correspondence in complex lasso proteins

2015-07 to 2016-06 | Grant
University of Warsaw, Faculty of Chemistry (Warsaw, PL)
GRANT_NUMBER:

120000-501/86-DSM-110200

Source: Self-asserted source
Pawel Dabrowski-Tumanski

Identification and characterization of proteins with link topology

Grant
Narodowe Centrum Nauki (National Science Centre) (Warsaw, PL)
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Works (30)

RapidDock: Unlocking Proteome-scale Molecular Docking

2024 | Preprint
Contributors: Rafał Powalski; Bazyli Klockiewicz; Maciej Jaśkowski; Bartosz Topolski; Paweł Dąbrowski-Tumański; Maciej Wiśniewski; Łukasz Kuciński; Piotr Miłoś; Dariusz Plewczynski
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Theta‐curves in proteins

Protein Science
2024-09 | Journal article
Contributors: Pawel Dabrowski‐Tumanski; Dimos Goundaroulis; Andrzej Stasiak; Eric J. Rawdon; Joanna I. Sulkowska
Source: check_circle
Crossref

AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology

Molecules
2023-11-07 | Journal article
Contributors: Pawel Dabrowski-Tumanski; Andrzej Stasiak
Source: check_circle
Crossref
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Preferred source (of 2)‎

AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology

2023-08-24 | Preprint
Contributors: Pawel Dabrowski-Tumanski; Andrzej Stasiak
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Lasso Proteins—Unifying Cysteine Knots and Miniproteins

Polymers
2021-11-18 | Journal article
Contributors: Bartosz Ambroży Greń; Pawel Dabrowski-Tumanski; Wanda Niemyska; Joanna Ida Sulkowska
Source: check_circle
Crossref
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A Topological Selection of Folding Pathways from Native States of Knotted Proteins

Symmetry
2021-09-10 | Journal article
Contributors: Agnese Barbensi; Naya Yerolemou; Oliver Vipond; Barbara I. Mahler; Pawel Dabrowski-Tumanski; Dimos Goundaroulis
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits

Journal of Chemical Information and Modeling
2021-07-26 | Journal article
Part of ISSN: 1549-9596
Part of ISSN: 1549-960X
Source: Self-asserted source
Pawel Dabrowski-Tumanski
grade
Preferred source (of 2)‎

Topoly: Python package to analyze topology of polymers

Briefings in Bioinformatics
2020-09-16 | Journal article
Part of ISSN: 1467-5463
Part of ISSN: 1477-4054
Source: Self-asserted source
Pawel Dabrowski-Tumanski

PyLink: a PyMOL plugin to identify links

Bioinformatics
2019-09-01 | Journal article
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Pawel Dabrowski-Tumanski
grade
Preferred source (of 2)‎

Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function

Polymers
2019-04-17 | Journal article
Contributors: Pawel Dabrowski-Tumanski; Bartosz Gren; Joanna I. Sulkowska
Source: check_circle
Crossref
grade
Preferred source (of 3)‎

Genus trace reveals the topological complexity and domain structure of biomolecules

Scientific Reports
2018 | Journal article
Part of ISSN: 2045-2322
Contributors: Sebastian Zając; Cody Geary; Ebbe Sloth Andersen; Pawel Dabrowski-Tumanski; Joanna I. Sulkowska; Piotr Sułkowski
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
Preferred source (of 3)‎

KnotProt 2.0: a database of proteins with knots and other entangled structures

Nucleic Acids Research
2018 | Journal article
Part of ISSN: 0305-1048
Contributors: Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis; Julien Dorier; Piotr Sułkowski; Kenneth C Millett; Eric J Rawdon; Andrzej Stasiak; Joanna I Sulkowska
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
Preferred source (of 3)‎

The exclusive effects of chaperonin on the behavior of proteins with 5 <inf>2</inf> knot

PLoS Computational Biology
2018 | Journal article
EID:

2-s2.0-85044785784

Contributors: Zhao, Y.; Dabrowski-Tumanski, P.; Niewieczerzal, S.; Sulkowska, J.I.
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Scopus - Elsevier

The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures

Reactive and Functional Polymers
2018-11 | Journal article
Part of ISSN: 1381-5148
Contributors: Pawel Dabrowski-Tumanski; Joanna I. Sulkowska
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
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GapRepairer: a server to model a structural gap and validate it using topological analysis.

Bioinformatics (Oxford, England)
2018-10 | Journal article
Contributors: Jarmolinska AI; Kadlof M; Dabrowski-Tumanski P; Sulkowska JI
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Europe PubMed Central
grade
Preferred source (of 2)‎

Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel.

The journal of physical chemistry. B
2018-10 | Journal article
Contributors: Dabrowski-Tumanski P; Piejko M; Niewieczerzal S; Stasiak A; Sulkowska JI
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Europe PubMed Central
grade
Preferred source (of 2)‎

The Exclusive Effects of Chaperonin on the Free Energy Landscape of Proteins with Complex Knots

Biophysical Journal
2018-02 | Journal article
Part of ISSN: 0006-3495
Contributors: Joanna I. Sulkowska; Yani Zhao; Paweł Dabrowski-Tumanski; Szymon Niewieczerzal
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search

To Tie or Not to Tie? That Is the Question

Polymers
2017 | Journal article
Part of ISSN: 2073-4360
Source: Self-asserted source
Pawel Dabrowski-Tumanski
grade
Preferred source (of 4)‎

PyLasso: a PyMOL plugin to identify lassos

Bioinformatics
2017-08 | Journal article
Part of ISSN: 1367-4803
Contributors: Aleksandra M Gierut; Wanda Niemyska; Pawel Dabrowski-Tumanski; Piotr Sułkowski; Joanna I Sulkowska; Alfonso Valencia
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
Preferred source (of 2)‎

Topological knots and links in proteins

Proceedings of the National Academy of Sciences
2017-03-09 | Journal article
Contributors: Pawel Dabrowski-Tumanski; Joanna I. Sulkowska
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
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LinkProt: a database collecting information about biological links

Nucleic Acids Research
2017-01-04 | Journal article
Contributors: Pawel Dabrowski-Tumanski; Aleksandra I. Jarmolinska; Wanda Niemyska; Eric J. Rawdon; Kenneth C. Millett; Joanna I. Sulkowska
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

LassoProt: server to analyze biopolymers with lassos

Nucleic acids research
2016 | Journal article
EID:

2-s2.0-85016093558

Contributors: Dabrowski-Tumanski, P.; Niemyska, W.; Pasznik, P.; Sulkowska, J.I.
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Scopus - Elsevier

Complex lasso: new entangled motifs in proteins

Scientific Reports
2016-11 | Journal article
Contributors: Wanda Niemyska; Pawel Dabrowski-Tumanski; Michal Kadlof; Ellinor Haglund; Piotr Sułkowski; Joanna I. Sulkowska
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
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In Search of Functional Advantages of Knots in Proteins

PLOS ONE
2016-11-02 | Journal article
Contributors: Pawel Dabrowski-Tumanski; Andrzej Stasiak; Joanna I. Sulkowska; Eugene A. Permyakov
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search
grade
Preferred source (of 2)‎

LinkProt: a database collecting information about biological links.

2016-10 | Journal article
Contributors: Dabrowski-Tumanski P; Jarmolinska AI; Niemyska W; Rawdon EJ; Millett KC; Sulkowska JI
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Europe PubMed Central

LassoProt: server to analyze biopolymers with lassos.

2016-04 | Journal article
Contributors: Dabrowski-Tumanski P; Niemyska W; Pasznik P; Sulkowska JI
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Europe PubMed Central

Prediction of the optimal set of contacts to fold the smallest knotted protein.

Journal of physics. Condensed matter : an Institute of Physics journal
2015 | Journal article
WOSUID:

MEDLINE:26291339

Contributors: Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I
Source: Self-asserted source
Pawel Dabrowski-Tumanski via ResearcherID
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Determining critical amino acid contacts for knotted protein folding

TASK Quarterly: scientific bulletin of Academic Computer Centre in Gdansk
2014 | Conference paper
Source: Self-asserted source
Pawel Dabrowski-Tumanski

Efficient and Rapid Synthesis of Nucleoside Diphosphate Sugars from Nucleoside Phosphorimidazolides

European Journal of Organic Chemistry
2013 | Journal article
WOSUID:

WOS:000319398600004

Contributors: Dabrowski-Tumanski, Pawel; Kowalska, Joanna; Jemielity, Jacek
Source: Self-asserted source
Pawel Dabrowski-Tumanski via ResearcherID

Synthesis of nucleotide sugars and nucleoside 5'-phosphosulfates by MgCl2 mediated coupling

Collection Symposium Series
2011 | Conference paper
Contributors: Pawel Dabrowski-Tumanski; Joanna Kowalska; Agnieszka Osowniak; Jacek Jemielity
Source: Self-asserted source
Pawel Dabrowski-Tumanski via Crossref Metadata Search

Peer review (35 reviews for 12 publications/grants)

Review activity for Antibiotics. (3)
Review activity for Applied sciences. (2)
Review activity for Biology methods & protocols. (15)
Review activity for Cancers. (1)
Review activity for Chemical science. (1)
Review activity for Computational and Structural Biotechnology Journal (1)
Review activity for Encyclopedia. (1)
Review activity for International journal of molecular sciences. (1)
Review activity for Journal of chemical information and modeling. (1)
Review activity for Mathematics. (4)
Review activity for Nature communications (3)
Review activity for Pharmaceutics. (2)