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Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and...
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Towards the description of charge transfer states in solubilised LHCII using subsystem DFT
Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of...
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Model Setup and Procedures for Prediction of Enzyme Reaction Kinetics with QM-Only and QM:MM Approaches
The enzyme-catalyzed reactions are traditionally studied with experimental kinetic assays. The modern theoretical modeling techniques provide a...
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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions
Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on...
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Molecular Dynamics and Other HPC Simulations for Drug Discovery
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical...
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Reaction mechanism of formate dehydrogenase studied by computational methods
Formate dehydrogenases (FDHs) are metalloenzymes that catalyse the reversible conversion of formate to carbon dioxide. Since such a process may be...
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Existing HPC Methods and the Communication Lower Bounds for Distributed-Memory Computations for Mass Spectrometry-Based Omics Data
Mass spectrometry (MS)-based omics data analysis requires substantial time and resources which has necessitated the need for high-performance...
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Informatics: Tools and Databases in Drug Discovery
Modern drug discovery and development research are built on information or data that have been acquired over many years and are linked to studies on...
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N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods
We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N 2 bound state of...
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Novel antimicrobial cruzioseptin peptides extracted from the splendid leaf frog, Cruziohyla calcarifer
Antimicrobial peptides (AMPs) constitute part of a broad range of bioactive compounds present on diverse organisms, including frogs. Peptides,...
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Process Validation
The concept of process validation has emerged as a central tenet required to establish the purity and safety of cellular therapy products. Effective...
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Feeding kinematics and ethology of Blue Sharks, Prionace glauca (Carcharhiniformes: Carcharhinidae)
Kinematic and behavioral studies of feeding performance in large, pelagic sharks have historically been hindered by logistical limitations including...
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Poor Person’s pH Simulation of Membrane Proteins
pH conditions are central to the functioning of all biomolecules. However, implications of pH changes are nontrivial on a molecular scale. Though a...
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Analysis of Glycosyl-Enzyme Intermediate Formation in the Catalytic Mechanism of Influenza Virus Neuraminidase Using Molecular Modeling
AbstractUsing classical molecular dynamics, constant-pH molecular dynamics simulation, metadynamics, and combined quantum mechanical and molecular...
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Artificial intelligence to deep learning: machine intelligence approach for drug discovery
Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. However, low efficacy,...
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AI in drug development: a multidisciplinary perspective
AbstractThe introduction of a new drug to the commercial market follows a complex and long process that typically spans over several years and...
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Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision...
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Similar distribution of 15N labeled cattle slurry and mineral fertilizer in soil after one year
Targeted use of animal manures as a nitrogen (N) fertilizer is challenging because of their poorly predictable N fertilizer value. An enhanced...
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Quantum Chemical and QM/MM Models in Biochemistry
Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe...
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Conformational turn triggers regio-selectivity in the bioactivation of thiophene-contained compounds mediated by cytochrome P450
In the present work, we performed Density Functional Theory calculations to explore the bioactivation mechanism of thiophene-containing molecules...
