FRAGSITE: a fragment-based approach for virtual ligand screening

H Zhou, H Cao, J Skolnick - Journal of chemical information and …, 2021 - ACS Publications
To reduce time and cost, virtual ligand screening (VLS) often precedes experimental ligand
screening in modern drug discovery. Traditionally, high-resolution structure-based docking …

FRAGSITE2: A structure and fragment‐based approach for virtual ligand screening

H Zhou, J Skolnick - Protein Science, 2024 - Wiley Online Library
Protein function annotation and drug discovery often involve finding small molecule binders.
In the early stages of drug discovery, virtual ligand screening (VLS) is frequently applied to …

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 …

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

H Zhou, H Cao, J Skolnick - Journal of chemical information and …, 2018 - ACS Publications
Computational approaches for predicting protein–ligand interactions can facilitate drug lead
discovery and drug target determination. We have previously developed a …

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

M Brylinski, J Skolnick - PLoS computational biology, 2009 - journals.plos.org
Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In
practice, virtual screening approaches have a number of limitations, and the development of …

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 …

Ligity: A non-superpositional, knowledge-based approach to virtual screening

JP Ebejer, PW Finn, WK Wong… - Journal of chemical …, 2019 - ACS Publications
We present Ligity, a hybrid ligand-structure-based, non-superpositional method for virtual
screening of large databases of small molecules. Ligity uses the relative spatial distribution …

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 …

Multiple structures for virtual ligand screening: defining binding site properties-based criteria to optimize the selection of the query

N Ben Nasr, H Guillemain, N Lagarde… - Journal of chemical …, 2013 - ACS Publications
Structure based virtual ligand screening (SBVLS) methods are widely used in drug
discovery programs. When several structures of the target are available, protocols based …

PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity

A Roy, B Srinivasan, J Skolnick - Journal of chemical information …, 2015 - ACS Publications
Often in pharmaceutical research the goal is to identify small molecules that can interact with
and appropriately modify the biological behavior of a new protein target. Unfortunately, most …