ArticleBMC bioinformatics2011
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography.Journal of chemical information and modeling · 2024Article
- Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins.Journal of chemical information and modeling · 2022Article
- An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease.Frontiers in molecular biosciences · 2021Article
- AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters.Journal of chemical information and modeling · 2020Article
- Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.Journal of computer-aided molecular design · 2019Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- Functional Evolution of Proteins.Proteins · 2019Article
- Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.Journal of computer-aided molecular design · 2019Article
- Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.Journal of structural and functional genomics · 2015Article
- Increasing the structural coverage of tuberculosis drug targets.Tuberculosis (Edinburgh, Scotland) · 2015Article
- Structural biology and chemistry of protein arginine methyltransferases.MedChemComm · 2014Review
- Ligand binding site similarity identification based on chemical and geometric similarity.The protein journal · 2013Article
- ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.Journal of chemical information and modeling · 2012Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB.
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Registered trials
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