A5070820751- Protein Structure and Dynamics
- Service-Oriented Architecture and Web Services
- Biochemical and Structural Characterization
- Enzyme Structure and Function
- Blind Source Separation Techniques
- Neural Networks and Applications
- Ubiquitin and proteasome pathways
- Business Process Modeling and Analysis
- Distributed and Parallel Computing Systems
- Semantic Web and Ontologies
- Cloud Computing and Resource Management
- Management and Organizational Practices
- Advanced Proteomics Techniques and Applications
- Geometric and Algebraic Topology
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced Electron Microscopy Techniques and Applications
- Biomimetic flight and propulsion mechanisms
- Topological and Geometric Data Analysis
- Modeling, Simulation, and Optimization
- Parallel Computing and Optimization Techniques
- Aerospace Engineering and Energy Systems
- Face and Expression Recognition
- Intellectual Property Rights and Media
- Financial Risk and Volatility Modeling
SGH Warsaw School of Economics
2005-2025
University of Virginia
2024-2025
University of Warsaw
2018-2024
Państwowa Wyższa Szkoła Zawodowa w Ciechanowie
2004-2024
Orange (Poland)
2010
Texas Tech University
2009
The KnotProt 2.0 database (the updated version of the database) collects information about proteins which form knots and other entangled structures. New features in include characterization both probabilistic deterministic entanglements can be formed by disulfide bonds interactions via ions, a refined entanglement terms knotoids, identification so-called cysteine knots, possibility to analyze all or non-redundant set proteins, various technical updates. classifies represents their complexity...
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the (PDB). goal of PDBe-KB place macromolecular structure their biological context by developing standardised exchange formats integrating partner into a knowledge graph that can provide valuable insights. Since we described 2019, there have been significant...
The fact that proteins can have their chain formed in a knot is known for almost 30 years. However, as they are not common, only fraction of such available the Protein Data Bank. It was possible to assess importance and versatility up until now because we did access whole proteome an organism, let alone human one. arrival efficient machine learning methods protein structure prediction, AlphaFold RoseTTaFold, changed that. We analyzed all from (over 20,000) determined with search knots found...
Abstract The increasing role of topology in (bio)physical properties matter creates a need for an efficient method detecting the (bio)polymer. However, existing tools allow one to classify only simplest knots and cannot be used automated sample analysis. To answer this need, we created Topoly Python package. This package enables distinguishing knots, slipknots, links spatial graphs through calculation different topological polynomial invariants. It also create minimal spanning surface on...
AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. has two main functions: (i) providing researchers with webserver for analyzing knotting their own AlphaFold predictions and (ii) database of from the 21 proteomes which have been published prior to 2022. The defined probabilistic fashion. complexity proteins presented form matrix diagram shows users knot type entire polypeptide chain each its subchains. dominant...
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic intense research. Capitalizing on the vast collection structure predictions offered by AlphaFold (AF), this study computationally examines entire UniProt database create robust dataset knotted unknotted proteins. Utilizing dataset, we develop machine learning (ML) model capable accurately predicting presence knots in structures solely from amino acid...
A global analysis of protein crystal structures in the Protein Data Bank (PDB) using a newly developed computational approach reveals many pairs with (nearly) identical main-chain coordinates. Such cases are identified and analyzed, showing that duplication is possible since PDB does not currently have tools or mechanisms would detect potentially duplicate submissions. Some duplicated entries represent modeling efforts ligand binding masquerade as experimentally determined structures. We...
The availability of 3D protein models is rapidly increasing with the development structure prediction algorithms. With expanding data, new ways analysis, especially topological those predictions are becoming necessary. Here, we present updated version AlphaKnot service that provides a straightforward way analyzing topology. It was designed specifically to determine knot types predicted models, however, it can be used for all structures, including ones solved experimentally. 2.0 user's...
Abstract Studying complex protein knots can provide new insights into potential knot folding mechanisms and other fundamental aspects of why how proteins knot. This paper presents results a systematic analysis the 3D structure with 6-crossings predicted by artificial intelligence program AlphaFold 2. Furthermore, using coarse-grained native based model, we found that three representative self tie to 6 3 knot, most in thus far. Because it is not twist cannot be folded via simple mechanism...
Federated computing environments offer requestors the ability to dynamically invoke services offered by collaborating providers in virtual service network. Without an efficient resource management, however, assignment of customer's requests cannot be optimized and high reliability without relevant SLA guarantees. We propose a new SLA-based serviceable metacomputing environment (SERVME) capable matching based on QoS requirements performing autonomic provisioning deprovisioning according...
The 'Genus for biomolecules' database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins RNA chains, which is captured by the genus a given chain its subchains. For each biomolecule, this shown in form trace plot, as well matrix diagram. We assemble such all structures deposited Protein Data Bank (PDB). This presents also various statistics extensive biological function analyzed biomolecules. regularly self-updating, once new are PDB....
Abstract AlphaFold is a new, highly accurate machine learning protein structure prediction method that outperforms other methods. Recently this was used to predict the of 98.5% human proteins. We analyze here these AlphaFold-predicted proteins for presence knots. found proteome contains 65 robustly knotted proteins, including most complex type knot yet reported in That type, denoted 6 3 mathematical notation, would necessitate more folding path than any characterized date. In some cases...
The absence of solvent molecules in high-resolution protein crystal structure models deposited the Protein Data Bank (PDB) contradicts fact that, for proteins crystallized from aqueous media, water are always expected to bind surface, as well some sites interior. An analysis contents PDB indicated that ratio number amino-acid residues exceeds 1.5 atomic resolution structures, decreasing 0.25 at around 2.5 Å resolution. Nevertheless, almost 800 structures determined a or higher found current...
The aim of this paper is to present a new Non-negative Matrix Factorization (NMF) algorithm based on Log-Quad divergence, and demonstrate its application the separation latent destructive components contained in prediction results multi-model approach. We provide an example real economic problem, i.e. forecasting electricity consumption basis information about hourly use Poland period 1988–1997. evaluated compared method with other blind signal (source) techniques, such as Independent...
Abstract Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles remain a topic intense research. Capitalizing on the vast collection structure predictions offered by AlphaFold, this study computationally examines entire UniProt database to create robust dataset knotted unknotted proteins. Utilizing dataset, we develop machine learning model capable accurately predicting presence knots in structures solely from amino acid sequences,...
Federated metacomputing environments allow requesters to dynamically invoke services offered by collaborating providers in the virtual service network.They evolve into metaoperating systems that form an intermediary layer between metaprograms -programs written terms of other programs -and metacomputer composed services.These require resource management efficiently handle assignment customer's requests and offer high reliability SLA guarantees.This paper presents SLA-based asynchronous...