Results 71 to 80 of about 36,254 (282)

Discovery of YopE Inhibitors by Pharmacophore-Based Virtual Screening and Docking [PDF]

ISRN Bioinformatics, 2013
Gram-negative bacteria Yersinia secrete virulence factors that invade eukaryotic cells via type III secretion system. One particular virulence member, Yersinia outer protein E (YopE), targets Rho family of small GTPases by mimicking regulator GAP protein activity, and its secretion mainly induces cytoskeletal disruption and depolymerization of actin ...
Gizem Ozbuyukkaya, Elif Ozkirimli Olmez, Kutlu O. Ulgen   +2 more
openaire   +2 more sources

Bioinformatics: A rational combine approach used for the identification and in-vitro activity evaluation of potent β-Glucuronidase inhibitors.

PLoS ONE, 2018
Identification of hotspot drug-receptor interactions through in-silico prediction methods (Pharmacophore mapping, virtual screening, 3DQSAR, etc), is considered as a key approach in drug designing and development process.
Maria Yousuf, Nimra Naveed Shaikh, Zaheer Ul-Haq, M Iqbal Choudhary   +3 more
doaj   +1 more source

Similarity-based data mining in files of two-dimensional chemical structures using fingerprint measures of molecular resemblance [PDF]

, 2011
This paper reviews the use of measures of intermolecular similarity for processing databases of chemical structures, which play an important role in the discovery of new drugs by the pharmaceutical industry.
Willett, P.
core   +1 more source

Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target

Journal of Biomolecular Structure and Dynamics, 2020
Since its first report in December 2019 from China, the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 5.59 million, and claiming the lives of more than 0.35 million individuals across the globe.
K. G. Arun, C. S. Sharanya, J. Abhithaj, Dileep Francis, Chittalakkottu Sadasivan   +4 more
semanticscholar   +1 more source

Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study

Natural Product Communications, 2016
A single, merged pharmacophore hypothesis is derived combining 2000 pharmacophore models obtained during a 20 ns molecular dynamics simulation of a protein-ligand complex with one pharmacophore model derived from the initial PDB structure.
Marcus Wieder, Ugo Perricone, Thomas Seidel, Thierry Langer   +3 more
doaj   +1 more source

Visual and computational analysis of structure-activity relationships in high-throughput screening data [PDF]

, 2001
Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent
Agrafiotis, Agrafiotis, Ahlberg, Ajay, Ajay, Bayada, Bemis, Bernard, Bonabeau, Brown, Calvert, Card, Chen, Chen, Cho, Christianini, Clark, Clark, Cox, Duda, Edwards, Engels, Frimurer, Gao, Garrido, Ghose, Gillet, Gillet, Hand, Hann, Haupts, Hayward, Hertzberg, Izrailev, Jiang, Jones-Hertzog, Kirew, Kobayashi, Kohonen, Ladd, Lee, Lepre, Martin, Mason, Mello, Meyer, Miller, Mitchell, Oprea, Peter Gedeck, Peter Willett, Poroikov, Rhodes, Roberts, Roberts, Ros, Rusinko, Sadowski, Sadowski, Scherf, Sheridan, Shi, Stanton, Su, Teague, Thompson, Tropsha, Tufte, Tufte, Wagener, Walters, Wang, Wedin, Xie, Xu, Zupan   +75 more
core   +1 more source

Revisiting Target‐Aware de novo Molecular Generation with TarPass: Between Rational Design and Texas Sharpshooter

Advanced Science, EarlyView.
TarPass provides a rigorous benchmark for target‐aware de novo molecular generation by jointly evaluating protein‐ligand interactions, molecular plausibility, and drug‐likeness on 18 well‐studied targets. Results show that current models often fail to consistently surpass random baseline in target‐specific enrichment, while post hoc multi‐tier virtual ...
Rui Qin, Zijie Chen, Yurong Li, Meijing Fang, Longji Shen, Yilong Su, Odin Zhang, Qinghan Wang, Qun Su, Jike Wang, Tingjun Hou, Yu Kang   +11 more
wiley   +1 more source

PharmacoForge: pharmacophore generation with diffusion models

Frontiers in Bioinformatics
Structure-based drug design (SBDD) is enhanced by machine learning (ML) to improve both virtual screening and de novo design. Despite advances in ML tools for both strategies, screening remains bounded by time and computational cost, while generative ...
Emma L. Flynn, Emma L. Flynn, Riya Shah , Ian Dunn , Ian Dunn , Rishal Aggarwal , Rishal Aggarwal , David Ryan Koes    +7 more
doaj   +1 more source

Evaluation of machine-learning methods for ligand-based virtual screening [PDF]

, 2007
Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier (NBC) methods for this purpose ...
A Bender, A Bender, A Bender, A Ormerod, A Ormerod, AE Klon, AM Capelli, AR Leach, B Chen, Beining Chen, C Williams, D Hand, D Rogers, D Wilton, DA Cosgrove, David J. Wood, DB Kitchen, DE Clark, DJ Hand, DJ Wilton, DM Hawkins, E Parzen, FL Stahura, G Harper, G Redl, G Schneider, George Papadatos, H Eckert, H Kubinyi, HM Berman, J Aitchison, J Bajorath, J Delaney, J Hert, J Hert, J Hert, JC Saeh, L Hodes, L Hodes, L Hodes, M Congreve, M Glick, M Glick, M Wagener, M Whittle, N Christianini, N Nikolova, Nikolaus Stiefl, P Constans, P Domingos, P Willett, P Willett, P Willett, P Willett, P Willett, Paulette Greenidge, Peter Willett, Q Zhang, R P Sheridan, RD Brown, RD Brown, RD Cramer, RE Carhart, RO Duda, Robert F. Harrison, S Anzali, TJ McNeany, TM Mitchell, Xiao Qing Lewell, XY Xia, YC Martin, YC Martin   +71 more
core   +2 more sources

Accelerating Primary Screening of USP8 Inhibitors from Drug Repurposing Databases with Tree‐Based Machine Learning

Advanced Intelligent Discovery, EarlyView.
This study introduces a tree‐based machine learning approach to accelerate USP8 inhibitor discovery. The best‐performing model identified 100 high‐confidence repurposable compounds, half already approved or in clinical trials, and uncovered novel scaffolds not previously studied. These findings offer a solid foundation for rapid experimental follow‐up,
Yik Kwong Ng, Sharon Ai Er Lam, Wei Chun Lim, Hannah Hui Min Toh, Shi Jun Ang   +4 more
wiley   +1 more source