Special Issue "In-Silico Drug Design and In-Silico Screening"
A special issue of Molecules (ISSN 1420-3049).
Deadline for manuscript submissions: closed (31 March 2014)
Prof. Dr. Iwao Ojima
Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, USA
Interests: drug discovery; anticancer agents; antimicrobial agents; anti-inflammatory agents; enzyme inhibitors; computer-aided drug design; structure-based drug design
Prof. Dr. Robert C. Rizzo
Department of Applied Mathematics and Statistics, Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
Interests: structure-based drug design; docking; virtual screening; molecular dynamics; infectious disease
Computer modeling’s overall usefulness in the drug discovery process is well established. Such modeling at the atomic level is an integral part of the paradigm of "structure-based design." Computational approaches, such as docking, can be used to predict how a small molecule ligand binds to a target. Given the recent advances in large-scale computing, large ligand libraries on the order of several millions of compounds can be effectively screened in silico to identify promising drug leads (virtual screening) for experimental testing. The screening of smaller molecular fragments using computers is another powerful approach. This screening can be used to identify binding site "hotpots" for which specific regions can be targeted with specific functional groups that have good steric and energetic complementarity. Other computational methods, such as de novo design, provide unique leverage for the informed design of new ligands "from scratch", as well as refinement of current leads prior to organic synthesis. Importantly, an active area of research for many research groups is continued improvement of the algorithms controlling the sampling and scoring of the inter- and intra molecular degrees of freedom that define a ligand binding geometry (pose). In this Special Issue of Molecules entitled "In-Silico Drug Design and In-Silico Screening", we invite manuscript submissions that discuss both the development and the application of computational methods. Original research articles or reviews that combine computational predications with experimental testing and verification are especially welcome.
Dr. Robert C. Rizzo
Dr. Iwao Ojima
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed Open Access monthly journal published by MDPI.
- structure-based drug design
- computer-aided drug design
- in silico drug design
- virtual screening
- in silico screening
- lead discovery
- binding pose identification
- database enrichment
- drug discovery
Article: Inhibition and Biochemical Characterization of Methicillin-Resistant Staphylococcus aureus Shikimate Dehydrogenase: An in Silico and Kinetic Study
Molecules 2014, 19(4), 4491-4509; doi:10.3390/molecules19044491
Received: 6 February 2014; in revised form: 3 April 2014 / Accepted: 4 April 2014 / Published: 10 April 2014| Download PDF Full-text (2040 KB)
Article: Computational Redesign of Bacterial Biotin Carboxylase Inhibitors Using Structure-Based Virtual Screening of Combinatorial Libraries
Molecules 2014, 19(4), 4021-4045; doi:10.3390/molecules19044021
Received: 21 February 2014; in revised form: 19 March 2014 / Accepted: 25 March 2014 / Published: 2 April 2014| Download PDF Full-text (4483 KB)
Article: Theoretical Study on the Allosteric Regulation of an Oligomeric Protease from Pyrococcus horikoshii by Cl− Ion
Molecules 2014, 19(2), 1828-1842; doi:10.3390/molecules19021828
Received: 19 December 2013; in revised form: 23 January 2014 / Accepted: 27 January 2014 / Published: 7 February 2014| Download PDF Full-text (2217 KB)
Article: The Effect of Conformational Variability of Phosphotriesterase upon N-acyl-L-homoserine Lactone and Paraoxon Binding: Insights from Molecular Dynamics Studies
Molecules 2013, 18(12), 15501-15518; doi:10.3390/molecules181215501
Received: 6 November 2013; in revised form: 3 December 2013 / Accepted: 6 December 2013 / Published: 12 December 2013| Download PDF Full-text (3026 KB)
Last update: 26 September 2013