PL-PatchSurfer2: improved local surface matching-based virtual screening method that is tolerant to target and ligand structure variation
WH Shin, CW Christoffer, J Wang… - Journal of chemical …, 2016 - ACS Publications
Virtual screening has become an indispensable procedure in drug discovery. Virtual
screening methods can be classified into two categories: ligand-based and structure-based …
screening methods can be classified into two categories: ligand-based and structure-based …
PatchSurfers: Two methods for local molecular property-based binding ligand prediction
Protein function prediction is an active area of research in computational biology. Function
prediction can help biologists make hypotheses for characterization of genes and help …
prediction can help biologists make hypotheses for characterization of genes and help …
Ligand-based virtual screening under partial shape constraints
MM von Behren, M Rarey - Journal of computer-aided molecular design, 2017 - Springer
Ligand-based virtual screening has proven to be a viable technology during the search for
new lead structures in drug discovery. Despite the rapidly increasing number of published …
new lead structures in drug discovery. Despite the rapidly increasing number of published …
ReverseScreen3D: a structure-based ligand matching method to identify protein targets
SL Kinnings, RM Jackson - Journal of chemical information and …, 2011 - ACS Publications
Ligand promiscuity, which is now recognized as an extremely common phenomenon, is a
major underlying cause of drug toxicity. We have developed a new reverse virtual screening …
major underlying cause of drug toxicity. We have developed a new reverse virtual screening …
Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
A Bender, HY Mussa, GS Gill… - Journal of medicinal …, 2004 - ACS Publications
A novel method (MOLPRINT 3D) for virtual screening and the elucidation of ligand− receptor
binding patterns is introduced that is based on environments of molecular surface points …
binding patterns is introduced that is based on environments of molecular surface points …
FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach
H Zhou, J Skolnick - Journal of chemical information and modeling, 2013 - ACS Publications
Virtual ligand screening is an integral part of the modern drug discovery process. Traditional
ligand-based, virtual screening approaches are fast but require a set of structurally diverse …
ligand-based, virtual screening approaches are fast but require a set of structurally diverse …
Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site
SI Virtanen, OT Pentikäinen - Journal of chemical information …, 2010 - ACS Publications
The protein structure-based virtual screening is typically accomplished using a molecular
docking procedure. However, docking is a fairly slow process that is limited by the available …
docking procedure. However, docking is a fairly slow process that is limited by the available …
Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket
In this report, we present a novel virtual high-throughput screening methodology to assist in
computer-aided drug discovery. Our method, designated as SLIM, involves ligand-free …
computer-aided drug discovery. Our method, designated as SLIM, involves ligand-free …
Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets
Virtual screening is one of the major tools used in computer-aided drug discovery. In
structure-based virtual screening, the scoring function is critical to identifying the correct …
structure-based virtual screening, the scoring function is critical to identifying the correct …
EViS: An Enhanced Virtual Screening Approach Based on Pocket–Ligand Similarity
W Zhang, J Huang - Journal of Chemical Information and …, 2022 - ACS Publications
Virtual screening (VS) is a popular technology in drug discovery to identify a new scaffold of
actives for a specific drug target, which can be classified into ligand-based and structure …
actives for a specific drug target, which can be classified into ligand-based and structure …