Article
Biochemistry & Molecular Biology
Roman A. Laskowski
Summary: PDBsum1 is a standalone set of programs that allows for in-house processing and indefinite retention of structural analysis results, similar to the functionalities of the PDBsum web server.
Article
Thermodynamics
Etoju Jacob, Hooman Farzaneh
Summary: This study presents the dynamic modeling and simulation of an off-grid DC microgrid system, and validates the model through real-time experiments. The results show that the microgrid system can effectively meet the load under different meteorological conditions, with a high sufficiency factor.
ENERGY CONVERSION AND MANAGEMENT
(2022)
Article
Chemistry, Physical
Lara Callea, Laura Bonati, Stefano Motta
Summary: A protocol combining SMD and metadynamics was developed for studying ligand binding processes, providing satisfactory results in identifying preferred entrance pathways and features of bound states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Bence Bruncsics, Wesley J. Errington, Casim A. Sarkar
Summary: This article introduces an application suite called MVsim, which utilizes a configurational network model to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena. Research shows that MVsim can accurately simulate both monospecific and multispecific multivalent ligand-receptor interactions, providing conceptual insights into multivalent systems.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Cecilia M. S. Alvares, Guillaume Maurin, Rocio Semino
Summary: In this study, the effectiveness of the MARTINI particle-based coarse graining approach in modeling the ZIF-8 metal-organic framework was evaluated. The results showed that the MARTINI force fields successfully captured the structure of the framework, except for the MARTINI 2.0 models with less coarse mapping. The choice of bead flavors within a particular MARTINI version had minimal impact on the simulated properties of the empty framework. None of the coarse-grained models could capture amorphization or the swing effect in MD simulations. The importance of proper Lennard-Jones parametrization for modeling guest-MOF and MOF-MOF interactions was highlighted.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
Charles Christoffer, Daisuke Kihara
Summary: Proteins and nucleic acids play crucial roles in various cellular processes, and their interactions are of great importance. Understanding the mechanisms of these interactions requires considering the 3D atomic structures of protein-nucleic acid complexes. When experimental structures are not available, protein docking can generate useful models computationally. However, traditional protein docking methods often have limitations in considering large-scale flexibility. Our previous work introduced a flexible protein docking method, Flex-LZerD, which can model ordered proteins undergoing significant conformational changes and is compatible with nucleic acids. In this study, we further demonstrate the ability of Flex-LZerD to model interactions between proteins and nucleic acids, showing an expanded range of interactions and conformational changes compared to previous methods.
Article
Chemistry, Physical
G. Medrano, E. Bainglass, O. Andreussi
Summary: Continuum solvation models are important in condensed matter simulations to characterize materials interfaces in wet electrified environments at reduced computational cost. However, implementing these models in plane-wave simulation packages for complex and heterogeneous environments is still challenging. This study proposes a double-cell formalism to address these challenges by separating the simulation cell for the continuum environment from the one for the electronic-structure simulation, allowing for larger simulation cell without increasing computational time.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson
Summary: We introduce Catalyst.jl, a flexible Julia library for modeling and simulating chemical reaction networks (CRNs) with high performance. Through comprehensive benchmarks, we demonstrate that Catalyst is much faster than other tools. It can be used as both a domain-specific language and an intermediate representation for encoding and manipulating CRN models symbolically.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Mathematical & Computational Biology
Dawei Ren, Xiaodong Zhang, Shaojuan Lei, Zehua Bi
Summary: This paper proposes a flexible simulation study of production system personnel based on mixed modeling to analyze the influence of personnel flexibility on the flexibility of the production system. The study establishes flexible evaluation index and simulation model to optimize the organization and configuration of the production system. Findings reveal that multi-energy and personnel cooperation significantly impact the flexibility of the production system, with multi-energy production teams showing improved flexibility in various dimensions compared to professional production teams in fluctuating production environments.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Green & Sustainable Science & Technology
Shanghui Yang, Xiaowei Deng, Jun Yang
Summary: This study compares three foundation modeling approaches for predicting the dynamic behavior of offshore wind turbines. It finds that the distributed spring model can provide a relatively accurate prediction of foundation stiffness, while the apparent fixity model underestimates it significantly. Additionally, the finite element model of the soil-pile system is more sensitive to soil densification and pile embedded depth, while the apparent fixity model shows higher sensitivity to pile diameter and thickness.
Article
Multidisciplinary Sciences
Norbert Ankri, Dominique Debanne
Summary: Channel noise caused by rapid transitions of protein channels is the dominant source of electrical noise causing membrane-potential fluctuations. Monte Carlo-based algorithm for simulating ion channel noise with few random numbers is more accurate than the Markovian method and stochastic differential equation methods. The fast Monte Carlo (FMC) model can accurately simulate channel noise regardless of the number of channels.
Article
Computer Science, Artificial Intelligence
Wei Chen, Hongjun Wang, Zhiguo Long, Tianrui Li
Summary: Co-clustering methods utilize the correlation between samples and attributes to explore the co-occurrence structure in data, playing a significant role in gene expression analysis, image segmentation, and document clustering. Existing bipartite graph partition-based co-clustering methods have high time complexity and the same number of row and column clusters. To address these problems, this paper proposes a novel fast flexible bipartite graph model (FBGPC) that directly constructs the bipartite graph using the original matrix and utilizes the inflation operation to partition the graph and learn the co-occurrence structure. Hierarchical clustering is then used to obtain the clustering results based on the relationship of the co-occurrence structure.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Angelo Felline, Michele Seeber, Francesca Fanelli
Summary: Structure graphs, known as Protein Structure Network (PSN), are cutting-edge tools for investigating macromolecular function. PSNtools is a standalone software that allows calculation and post-processing of PSN analyses. It can perform network comparisons and consensus calculations. Additionally, an updated version of the webPSN server enables interactive graphical analysis of PSN-MD.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Construction & Building Technology
Qi Zhou, Ryozo Ooka
Summary: The coupling of CFD and BES enables simultaneous consideration of indoor environment quality and building energy performance in architecture design. In this study, an innovative coupled simulation framework using a neural network for fast and accurate prediction of indoor air distribution is proposed. The framework demonstrates more reasonable results and significantly reduces calculation time compared to traditional coupled simulation methods.
BUILDING AND ENVIRONMENT
(2022)
Article
Biochemical Research Methods
William F. Anjos, Gabriel C. Lanes, Vasco A. Azevedo, Anderson R. Santos
Summary: GENPPI software allows for the prediction of interaction networks using predicted proteins from a genome, showing efficient and effective results. The software creates interaction networks that accurately reflect the evolutionary relationships between species.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Mateusz Kurcinski, Aleksandra Badaczewska-Dawid, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
Article
Biochemical Research Methods
Aleksandra E. Badaczewska-Dawid, Sebastian Kmiecik, Michal Kolinski
Summary: The three-stage molecular docking protocol for GPCR-peptide ligands produces high resolution models for the top-scored complexes, which can be further refined and improved to sub-angstrom accuracy through high-resolution refinement and minimization.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Daniel Szulczyk, Anna Bielenica, Piotr Roszkowski, Michal A. Dobrowolski, Wioletta Olejarz, Sebastian Kmiecik, Malgorzata Podsiad, Marta Struga
Summary: Twelve novel derivatives of N-(furan-2-ylmethyl)-1H-tetrazol-5-amine were synthesized and tested for antibacterial, antimycobacterial, and cytotoxic activities. Compound 6 showed the most promising results in antimicrobial studies, particularly inhibiting the growth of S. epidermidis strains. A pharmacophore model was established based on lead compounds from this and previous works.
Article
Biochemistry & Molecular Biology
Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Kolinski
Summary: The study introduces a new straightforward approach for protein docking sampling, involving large-scale backbone rearrangements in one protein and small backbone fluctuations in the other protein using Replica Exchange Monte Carlo dynamics. Acceptable quality models were obtained for a significant number of cases in simulations of 62 protein-protein complexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mateusz Zalewski, Sebastian Kmiecik, Michal Kolinski
Summary: This study proposes an MD-based scoring approach to identify high-accuracy protein-peptide models from CG docking simulations. The accuracy of the scoring can be significantly affected by the quality of the reconstructed protein receptor structures.
Article
Biochemistry & Molecular Biology
Piotr Roszkowski, Jolanta Szymanska-Majchrzak, Michal Kolinski, Sebastian Kmiecik, Malgorzata Wrzosek, Marta Struga, Daniel Szulczyk
Summary: Eleven novel imide-tetrazoles were synthesized and screened for antimicrobial activity. Compounds 1-3 showed the most promising results with minimal inhibitory concentration values within the range of 0.8-3.2 μg/mL. These compounds exhibited higher activity than the reference drug in some cases. They also inhibited the growth of clinical Staphylococci panels with MIC values of 0.8 μg/mL. Further studies on the binding modes of these compounds suggest their potential as novel antimicrobial drug candidates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Aleksandra E. Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik
Summary: This article utilizes the Aggrescan3D tool to analyze the aggregation properties of human protein structures predicted by AlphaFold, and presents the results in a database format. The A3D database provides detailed analysis of the structure-based aggregation propensity, along with graphical tools for visualization and interpretation of protein structure datasets. Users can also test the impact of selected mutations on protein solubility and stability using this database.
Article
Biochemistry & Molecular Biology
Alicja Chrzanowska, Marta Struga, Piotr Roszkowski, Michal Kolinski, Sebastian Kmiecik, Karolina Jalbrzykowska, Anna Zabost, Joanna Stefanska, Ewa Augustynowicz-Kopec, Malgorzata Wrzosek, Anna Bielenica
Summary: Novel conjugates of moxifloxacin with fatty acids were synthesized and found to have stronger cytotoxic potential than the parent drug. Some of these conjugates showed high cytotoxicity against prostate cancer cells. Additionally, they exhibited activity against standard and clinical bacterial strains, as well as mycobacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra E. Badaczewska-Dawid, Chandran Nithin, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik
Summary: Mapiya is a web server that integrates multiple functionalities for the analysis and visualization of biomolecular interactions in various biological systems, providing an easy-to-use interface.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Tomasz Szostek, Daniel Szulczyk, Jolanta Szymanska-Majchrzak, Michal Kolinski, Sebastian Kmiecik, Dagmara Otto-Slusarczyk, Aleksandra Zawodnik, Eliza Rajkowska, Kinga Chaniewicz, Marta Struga, Piotr Roszkowski
Summary: Sixteen new Ciprofloxacin derivatives were designed and synthesized, and their antimicrobial and cytotoxic activities were evaluated. Derivative 12 exhibited the highest antimicrobial activity and showed good activity against cancer cells without cytotoxicity to normal cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Marta Struga, Piotr Roszkowski, Anna Bielenica, Dagmara Otto-Slusarczyk, Karolina Stepienn, Joanna Stefanska, Anna Zabost, Ewa Augustynowicz-Kopec, Michal Kolinski, Sebastian Kmiecik, Alina Myslovska, Malgorzata Wrzosek
Summary: A novel series of N-acylated ciprofloxacin conjugates were synthesized and screened as potential antimicrobial agents. Some of the conjugates showed higher or comparable activity to ciprofloxacin against selected Gram-positive and Gram-negative strains. Additionally, these compounds exhibited strong inhibitory effects against Mycobacterium tuberculosis isolates and antiproliferative activities against prostate cancer cells.
Article
Chemistry, Physical
Aidan P. Holman, Kimberly Quinn, Rakesh Kumar, Sebastian Kmiecik, Abid Ali, Dmitry Kurouski
Summary: Long-chain unsaturated and polyunsaturated fatty acids are important components of cell membranes and are involved in cell signaling and metabolism. They are widely used as food supplements but their role in the self-assembly of misfolded proteins is still unclear.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Biochemistry & Molecular Biology
Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
