Visualizing The Future of Molecular Graphics

Olson, Arthur J.; Pique, Michael E.

doi:10.1080/10629369808039142

Cited by 7 publications

(5 citation statements)

References 36 publications

(26 reference statements)

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“…Molecular and genomic methods are anticipated to influence the direction of medical microbiology in the future. With these methods, infectious illness diagnoses can be made more quickly and precisely, which can lead to better patient outcomes [52,53]. Additionally, in light of the increasing prevalence of antibiotic resistance, molecular and genomic techniques can be used to discover bacterial strains that are resistant to antibiotics [54].…”

Section: Future Of Molecular and Genomic Approachesmentioning

confidence: 99%

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Goyal,

Bankar,

Mishra

et al. 2023

Cureus

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Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.

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Section: Future Of Molecular and Genomic Approachesmentioning

confidence: 99%

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Goyal,

Bankar,

Mishra

et al. 2023

Cureus

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“…These can be red independently from the rest of the manuscript. We refer to the literature for more thoroughly reviews on the more technical aspects of molecular visualization (1,2,3,4,5,6,7,8,9,10). Also, the large number of visualization tools will not be reviewed or compared.…”

Section: Overview Of the Drug Design Processmentioning

confidence: 99%

Molecular visualization in the rational drug design process

Keil¹,

Marhöfer²,

Rohwer³

et al. 2009

Front Biosci

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The visualization of molecular scenarios on an atomic level can help to interpret experimental and theoretical findings. This is demonstrated in this review article with the specific field of drug design. State-of-the-art visualization techniques are described and applied to the different stages of the rational design process. Numerous examples from the literature, in which visualization was used as a major tool in the data analysis and interpretation, are provided to show that images are not only useful for drawing the attention of the reader to a specific paper in a scientific journal.

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“…Chem Biol Drug Des 2006; 67: [5][6][7][8][9][10][11][12]to be in the 'native binding mode,' the R1 groups are expected to interact with the hydrophobic pocket of p38. The R2 portion of 1ouk-inh, on the other hand, is positioned in the vicinity of the adenine-binding site in the hinge region, whereas the R3 group interacts with the phosphate-binding region (P-loop).…”

Section: Structural Interaction Fingerprintsmentioning

confidence: 99%

“…For example, LIGPLOT generates twodimensional (2D) schematics of protein-small molecule complexes that describe the intermolecular interactions including the strengths of hydrogen bonds and hydrophobic interactions [5]. In addition to 2D approaches, a variety of sophisticated computer graphics programs such as InsightII (Accelrys Inc., Burlington, MA, USA), VIDA (Open Eye, Cambridge, MA, USA), Sybyl (Tripos Inc., St Louis, MO, USA), and Maestro (Schrodinger Inc., New York, NY, USA) are available for analyzing the 3D structure of proteins and their complexes [6]. Although these 2D and 3D approaches are useful when examining small numbers of structures, the analysis of large datasets is not feasible.…”

mentioning

confidence: 99%

Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes

Singh¹,

Deng

Narale

et al. 2005

Chem Biol Drug Des

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The combination of advances in structure-based drug design efforts in the pharmaceutical industry in parallel with structural genomics initiatives in the public domain has led to an explosion in the number of structures of protein-small molecule complexes structures. This information has critical importance to both the understanding of the structural basis for molecular recognition in biological systems and the design of better drugs. A significant challenge exists in managing this vast amount of data and fully leveraging it. Here, we review our work to develop a simple, fast way to store, organize, mine, and analyze large numbers of protein-small molecule complexes. We illustrate the utility of the approach to the management of inhibitor complexes from the protein kinase family. Finally, we describe our recent efforts in applying this method to the design of target-focused chemical libraries. Received 25 October 2005The past decade has witnessed a dramatic increase in the number of protein-small molecule complex structures from experimental as well as in silico approaches. Over 5000 small molecule complexes have been deposited in public databases [1], and it is likely that a much greater number have been determined within the pharmaceutical industry. With significant progress in structural genomics initiatives [2] and advances of high-throughput crystallography [3] and highthroughput NMR technology [4], the total number of structures will grow at an even greater speed. In parallel to the growth of experimentally determined structures, a wealth of in silico structural information is also being generated from virtual screening efforts. The ability to fully leverage this experimental and in silico information hinges on the ability to organize, analyze, and mine the structural data to both derive insights into molecular recognition in biological systems as well as facilitate the design of novel therapeutics.Several approaches exist for analyzing the interactions of proteinsmall molecule complexes. For example, LIGPLOT generates twodimensional (2D) schematics of protein-small molecule complexes that describe the intermolecular interactions including the strengths of hydrogen bonds and hydrophobic interactions [5]. In addition to 2D approaches, a variety of sophisticated computer graphics programs such as InsightII (Accelrys Inc., Burlington, MA, USA), VIDA (Open Eye, Cambridge, MA, USA), Sybyl (Tripos Inc., St Louis, MO, USA), and Maestro (Schrodinger Inc., New York, NY, USA) are available for analyzing the 3D structure of proteins and their complexes [6]. Although these 2D and 3D approaches are useful when examining small numbers of structures, the analysis of large datasets is not feasible. In addition to visual analysis of complexes, it is also common to use energy-based methods to evaluate how favorable the binding interactions are between a protein and a small molecule complex. These scoring methods are commonly used to rank and filter large datasets of virtual screening results [7]. Recent studies have demonst...

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Visualizing The Future of Molecular Graphics

Cited by 7 publications

References 36 publications

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Molecular visualization in the rational drug design process

Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes

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