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ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

L. M. C. Meireles, A. S. Domling, C. J. Camacho
2010 Nucleic Acids Research  
ANCHOR web server and database are freely available at  ...  ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design.  ...  UTILITY AND DISCUSSION Analysis of PPI hotspots for drug discovery In order for a small molecule to bind with high affinity to a given protein target, the molecule ideally needs to bury a substantial  ... 
doi:10.1093/nar/gkq502 pmid:20525787 pmcid:PMC2896143 fatcat:cqq66vauong4xmic5omr7mekf4

A Review on Computational Software Tools for Drug Design and Discovery

Jimish R. Patel, Hirak V. Joshi, Ujashkumar A. Shah, Jayvadan K. Patel
2022 Indo global journal of pharmaceutical sciences  
, homology modeling, 3D structure generator, Computational Crystallography, protein Database, and calculation software.  ...  Review article important for choice and application of wide-reaching used Drug Design software.©2022iGlobal Research and PublishingFoundation. All rights reserved.  ...  Docking Server is a web online server for molecular docking study of protein-ligand interaction. This software is easy to use and give a docking score.  ... 
doi:10.35652/igjps.2022.12006 fatcat:gcn3diavafbrvkrxhm3j7hwige

Considerations of Protein Subpockets in Fragment-Based Drug Design

Matthew Bartolowits, V. Jo Davisson
2015 Chemical Biology and Drug Design  
Further development of generalized methods for the discovery of similar protein-/ligand-binding sites and predicting the interaction profile of molecular fragments remains of high interest (19).  ...  The field of drug discovery has long struggled with the accurate prediction of a drug's cross-pharmaco-logic profile (15-18) and sideeffects.  ...  A web server such as ProBiS (83) is useful for detecting either global or local similarities between proteins and identifying structurally conserved binding sites on proteins of interest.  ... 
doi:10.1111/cbdd.12631 pmid:26307335 pmcid:PMC5464946 fatcat:htvtnl3ysbdnjcacexnbmtwcou

Structure-based prediction of protein allostery

Joe G Greener, Michael JE Sternberg
2018 Current Opinion in Structural Biology  
We also describe the search for cryptic binding pockets and attempts to design allostery into proteins.  ...  In order for the benefits of allostery to be taken advantage of, both for basic understanding of proteins and to develop new classes of drugs, the structure-based prediction of allosteric binding sites  ...  Acknowledgement This work was supported by Biotechnology and Biological Sciences Research Council grant BB/J014575/1.  ... 
doi:10.1016/j.sbi.2017.10.002 pmid:29080471 fatcat:lxfjcncgyza4lbwofbteux5gna

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

David Koes, Kareem Khoury, Yijun Huang, Wei Wang, Michal Bista, Grzegorz M. Popowicz, Siglinde Wolf, Tad A. Holak, Alexander Dömling, Carlos J. Camacho, Bin Xue
2012 PLoS ONE  
Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs).  ...  Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with  ...  Oltvai for useful comments on the manuscript. Philip Davidson, a MS student at CMU, predicted the top ranked ligand of GP41 shown in Figure 1 .  ... 
doi:10.1371/journal.pone.0032839 pmid:22427896 pmcid:PMC3299697 fatcat:inngxaidcnblvc5ezafseyqnuu

Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

Stephani Joy Y. Macalino, Shaherin Basith, Nina Abigail B. Clavio, Hyerim Chang, Soosung Kang, Sun Choi
2018 Molecules  
Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.  ...  This has progressively steered current research interests to understanding protein-protein interaction (PPI) systems that are related to a number of relevant diseases, such as cancer, neurological illnesses  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23081963 pmid:30082644 fatcat:e6cduopkq5gprcmwane7twfdam

Computational Prediction of Protein Hot Spot Residues

John Kenneth Morrow, Shuxing Zhang
2012 Current pharmaceutical design  
Design of therapeutic agents that interact with hot spot residues has proven to be a valid methodology in disrupting unwanted protein-protein interactions.  ...  Here we review the state of knowledge around protein-protein interactions, hot spots, and give an overview of multiple in silico prediction techniques of hot spot residues.  ...  Acknowledgments This work was supported in part by the US Department of Defense Concept Awards (BC085871), Grant # IRG-08-061-01 from the American Cancer Society and MDACC-UT Austin CTT-TI3D grants.  ... 
doi:10.2174/138161212799436412 pmid:22316154 pmcid:PMC3807665 fatcat:glhmapaayrdd3ojdnquzfuzbja

Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation

Shraddha Parate, Shailima Rampogu, Gihwan Lee, Jong Chan Hong, Keun Woo Lee
2021 Frontiers in Molecular Biosciences  
In the current investigation, the binding of RKIP with C-Raf was explored by knowledge-based protein-protein docking web-servers including HADDOCK and ZDOCK and a consensus binding mode of C-Raf/RKIP structural  ...  Moreover, per-residue energy contribution analysis of the equilibrated simulation trajectory by HawkDock and ANCHOR web-servers was conducted to characterize the key residues for the complex formation.  ...  Subsequently, we also identified druggable "hot spots" that can be targeted for future drug optimization by ANCHOR web-server.  ... 
doi:10.3389/fmolb.2021.655035 pmid:34124147 pmcid:PMC8194344 fatcat:vddo4lz5znd6vo3r2raidhdara

Computer aided drug designing platform towards the enigma SARS-CoV-2 spike protein of COVID-19

Miroslava, Vasil, Mahdi
2021 Zenodo  
The discovery of new drugs that could target this complex efficiently would be a very long, multi-step, and expensive process as every other drug discovery.  ...  in chemical libraries consisting of FDA approved or test drugs, and as well the natural compound based on essential oils and available information in the literature sources to select compounds interacting  ...  The active pocket amino acid residues were used based on a degenerated data from a web server pocket detection.  ... 
doi:10.5281/zenodo.5256608 fatcat:6dwl26vgsnd5rhz64adjmkjel4

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
Key words: virtual ligand screening, structure-based drug design, docking, scoring, drug discovery, protein-protein interaction.  ...  Among these methods, virtual ligand screening, protein-protein docking, structural predictions and druggable pocket predictions have become established techniques for hit discovery and optimization.  ...  Acknowledgments Supports from the Inserm institute and Inserm-Transfert are greatly appreciated.  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

Identification of Drug and Vaccine Target in Mycobacterium leprae: A Reverse Vaccinology Approach

Ekta Gupta, Shradheya R. R. Gupta, Ravi Ranjan Kumar Niraj
2019 International Journal of Peptide Research and Therapeutics  
Results from the present study could facilitate selecting M. leprae proteins for drug design as well as vaccine production pipelines in the future.  ...  The systematic workflow of the current study consists of a computational approach, where complete proteome of the bacteria is gradually reduced to find out few unique probable drug targets and reverse  ...  Acknowledgements The authors would like to acknowledge the Institutional Research Scientific Committee (IRSC) of Dr. B. Lal Institute of biotechnology for financial and infrastructural support.  ... 
doi:10.1007/s10989-019-09936-x fatcat:juphkwpsyvek7fknezbrmndbje

A platform for target prediction of phenotypic screening hit molecules

Nadine Homeyer, Ruud van Deursen, Bernardo Ochoa-Montaño, Kathrin Heikamp, Peter Ray, Fabio Zuccotto, Tom L. Blundell, Ian H. Gilbert
2019 Journal of Molecular Graphics and Modelling  
Many drug discovery programmes, particularly for infectious diseases, are conducted phenotypically.  ...  In a test that we performed, the platform was able to predict the targets of 60% of compounds investigated, where there was some similarity to a ligand in the protein database.  ...  In particular we would like to thank Jonathan Downward for setting up the hardware and software for the web and database servers. Appendix A.  ... 
doi:10.1016/j.jmgm.2019.107485 pmid:31836397 pmcid:PMC6983931 fatcat:cf7tdcsaenbvzlqa5gio3zd5gi

In-Silico Identification of the Best Compound Against Leishmania infantum: High Throughput Screening of All FDA Approved Drugs

Jasem Saki, Farnoush Shadnoush, Reza Arjmand, Fakher Rahim
2019 Turkish Journal of Parasitology  
Current in-silico research was designed and administered for the screening of 20000 Food and Drug Administration-approved drug compounds with the goal of finding promising drugs against lipophosphoglycan  ...  (LPG) and γ-glutamylcysteine synthetase (γ-GCS) of Leishmania infantum.  ...  Server (http://www.prosess.ca) web servers.  ... 
doi:10.4274/tpd.galenos.2019.6290 pmid:31865648 fatcat:w4mvdxgcunhjbgnwiblmgtz5gm

Significant Aspect of Rv0378 Gene of Mycobacterium tuberculosis H37Rv Reveals the PE_PGRS like Properties by Computational Approaches

Beg MA, Athar F, Meena LS
2019 Journal of Biotechnology and Biomedicine  
The major insights of this study include interaction study, modelling by using I-TASSER, validation of the model by RAMPAGE analysis and prediction of metal binding sites by using Insilico approaches.  ...  Interaction study by STRING shows that this protein interacts with its neighboring partner and secE2 protein which is a transporter protein.  ...  Acknowledgement The authors acknowledge financial support from the Department of Science and Technology-SERB, Council of Conflict of Interest There is no conflict of interest.  ... 
doi:10.26502/jbb.2642-9128007 fatcat:bmazfp6dazezjagzx2pgbl7ihi

Drug-Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Bruno O. Villoutreix, Melaine A. Kuenemann, Jean-Luc Poyet, Heriberto Bruzzoni-Giovanelli, Céline Labbé, David Lagorce, Olivier Sperandio, Maria A. Miteva
2014 Molecular Informatics  
We first introduce the field of proteinÀprotein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs.  ...  about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages.  ...  Rognan for the organization of the 2014 International Workshops in Chemoinformatics.  ... 
doi:10.1002/minf.201400040 pmid:25254076 pmcid:PMC4160817 fatcat:kryzjqycvrg5vd3surg4sdxrgy
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