Author details

Full Name

Brian Y Chen

Affiliation

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
34890136	DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity.	Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing	2022
36358939	HBcompare: Classifying Ligand Binding Preferences with Hydrogen Bond Topology.	Biomolecules	2022
36234723	Analysis of Protein-Protein Interactions for Intermolecular Bond Prediction.	Molecules	2022
35378834	DiffBond: A Method for Predicting Intermolecular Bond Formation.	Proceedings (IEEE Int Conf Bioinformatics Biomed)	2021
32489400	Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials.	Algorithms for Molecular Biology	2020
29414909	Exploring Protein Cavities through Rigidity Analysis.	Molecules	2018
28051901	Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity.	Journal of Computational Biology	2017
28230053	Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk.	Scientific Reports	2017
26335806	Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity.	Journal of Computational Biology	2015
25166865	VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.	PLoS Computational Biology	2014
24564934	An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.	BMC Structural Biology	2013
24384707	Isolating influential regions of electrostatic focusing in protein and DNA structure.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2013
22759583	Modeling regionalized volumetric differences in protein-ligand binding cavities.	Proteome Science	2012
22809380	A regionalizable statistical model of intersecting regions in protein-ligand binding cavities.	Journal of Bioinformatics and Computational Biology	2012
21672961	MarkUs: a server to navigate sequence-structure-function space.	Nucleic Acids Res	2011
27468109	A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function.	Mol Inform	2011
20459833	Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.	BMC Bioinformatics	2010
20814581	VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.	PLoS Comput Biol	2010
20034113	Mapping of ligand-binding cavities in proteins.	Proteins: Structure, Function and Bioinformatics	2010
18190718	Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.	BMC Bioinformatics	2008
17589966	Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction.	J Bioinform Comput Biol	2007
17951837	Composite motifs integrating multiple protein structures increase sensitivity for function prediction.	Comput Syst Bioinformatics Conf	2007
17691895	The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.	J Comput Biol	2007
16672239	Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.	Protein Sci	2006
17369649	Cavity-aware motifs reduce false positives in protein function prediction.	Comput Syst Bioinformatics Conf	2006
15759639	Algorithms for structural comparison and statistical analysis of 3D protein motifs.	Pac Symp Biocomput	2005