Publications by authors named "Ambrish Roy"

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QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
Fatima Zohra Smaili, Shuye Tian, Ambrish Roy, Meshari Alazmi, Stefan T Arold

Genomics Proteomics Bioinformatics· December 2021

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Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs.
Bharath Srinivasan, Sam Tonddast-Navaei, Ambrish Roy, Hongyi Zhou, Jeffrey Skolnick

Med Res Rev· March 2019

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Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects.
Peter M Eimon, Mostafa Ghannad-Rezaie, Gianluca De Rienzo, Amin Allalou, Yuelong Wu, Ambrish Roy

Nat Commun· January 2018

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PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.
Ambrish Roy, Bharath Srinivasan, Jeffrey Skolnick

J Chem Inf Model· August 2015

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Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.
Jeffrey Skolnick, Mu Gao, Ambrish Roy, Bharath Srinivasan, Hongyi Zhou

Bioorg Med Chem Lett· March 2015

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LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.
Ambrish Roy, Jeffrey Skolnick

Bioinformatics· February 2015

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The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson

Nat Methods· January 2015

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CANDO and the infinite drug discovery frontier.
Mark Minie, Gaurav Chopra, Geetika Sethi, Jeremy Horst, George White, Ambrish Roy

Drug Discov Today· September 2014

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Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment.
Jianyi Yang, Ambrish Roy, Yang Zhang

Bioinformatics· October 2013

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BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.
Jianyi Yang, Ambrish Roy, Yang Zhang

Nucleic Acids Res· January 2013

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COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.
Ambrish Roy, Jianyi Yang, Yang Zhang

Nucleic Acids Res· July 2012

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Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement.
Ambrish Roy, Yang Zhang

Structure· June 2012

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Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers.
Rajasree Menon, Ambrish Roy, Srayanta Mukherjee, Saveliy Belkin, Yang Zhang

J Proteome Res· December 2011

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Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
Dong Xu, Jian Zhang, Ambrish Roy, Yang Zhang

Proteins· December 2011

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A protocol for computer-based protein structure and function prediction.
Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang

J Vis Exp· November 2011

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Parkin, A Top Level Manager in the Cell's Sanitation Department.
Carolyn A Rankin, Ambrish Roy, Yang Zhang, Mark Richter

Open Biochem J· July 2011

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I-TASSER: a unified platform for automated protein structure and function prediction.
Ambrish Roy, Alper Kucukural, Yang Zhang

Nat Protoc· April 2010

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The role of covalent dimerization on the physical and chemical stability of the EC1 domain of human E-cadherin.
Maulik Trivedi, R Andrew Davis, Yumna Shabaik, Ambrish Roy, Gennady Verkhivker

J Pharm Sci· October 2009

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HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.
Yunqi Li, Ambrish Roy, Yang Zhang

PLoS One· August 2009

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Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: implications for function annotation based on homology searches and structural genomics.
Ambrish Roy, Narayanaswamy Srinivasan, Venkatraman S Gowri

In Silico Biol· July 2009

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