Ajay N. Jain

Publication Activity (10 Years)

Years Active: 1989-2024
Publications (10 Years): 10

Top Topics

Protein Structural

Shape Similarity

Prediction Error

Virtual Screening

Top Venues

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

J. Cheminformatics

Pacific Symposium on Biocomputing

Publications

Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design. J. Comput. Aided Mol. Des. 38 (1) (2024)
Ann E. Cleves, Ajay N. Jain, David A. Demeter, Zachary A. Buchan, Jeremy Wilmot, Erin N. Hancock
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product. J. Comput. Aided Mol. Des. 38 (1) (2024)
Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design. J. Comput. Aided Mol. Des. 37 (11) (2023)
Ann E. Cleves, Stephen R. Johnson, Ajay N. Jain
Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction. J. Chem. Inf. Model. 61 (12) (2021)
Ann E. Cleves, Ajay N. Jain
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket. J. Chem. Inf. Model. 60 (9) (2020)
Ann E. Cleves, Stephen R. Johnson, Ajay N. Jain
Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. J. Comput. Aided Mol. Des. 33 (10) (2019)
Ajay N. Jain, Ann E. Cleves, Qi Gao, Xiao Wang, Yizhou Liu, Edward C. Sherer, Mikhail Y. Reibarkh
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. J. Comput. Aided Mol. Des. 33 (6) (2019)
Ann E. Cleves, Ajay N. Jain
Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. J. Comput. Aided Mol. Des. 32 (7) (2018)
Ann E. Cleves, Ajay N. Jain
ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. J. Comput. Aided Mol. Des. 31 (5) (2017)
Ann E. Cleves, Ajay N. Jain
Extrapolative prediction using physically-based QSAR. J. Comput. Aided Mol. Des. 30 (2) (2016)
Ann E. Cleves, Ajay N. Jain
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. J. Comput. Aided Mol. Des. 29 (6) (2015)
Ann E. Cleves, Ajay N. Jain
Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes. J. Comput. Aided Mol. Des. 29 (2) (2015)
Emmanuel R. Yera, Ann E. Cleves, Ajay N. Jain
Prediction of Off-Target Drug Effects Through Data Fusion. Pacific Symposium on Biocomputing (2014)
Alexander Steudle, Rocco Varela, Ajay N. Jain
Surflex-QMOD: physically meaningful QSAR. J. Cheminformatics 6 (S-1) (2014)
Rocco Varela, Ann E. Cleves, Russell Spitzer, Ajay N. Jain
A structure-guided approach for protein pocket modeling and affinity prediction. J. Comput. Aided Mol. Des. 27 (11) (2013)
Russell Spitzer, Ajay N. Jain
Surflex-Dock: Docking benchmarks and real-world application. J. Comput. Aided Mol. Des. 26 (6) (2012)
Ajay N. Jain, Ann E. Cleves
Does your model weigh the same as a Duck? J. Comput. Aided Mol. Des. 26 (1) (2012)
Ajay N. Jain
QMOD: physically meaningful QSAR. J. Comput. Aided Mol. Des. 24 (10) (2010)
Ajay N. Jain
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J. Comput. Aided Mol. Des. 23 (6) (2009)
James J. Langham, Ajay N. Jain
Accurate and Interpretable Computational Modeling of Chemical Mutagenicity. J. Chem. Inf. Model. 48 (9) (2008)
Ajay N. Jain
Bias, reporting, and sharing: computational evaluations of docking methods. J. Comput. Aided Mol. Des. 22 (3-4) (2008)
Ann E. Cleves, Ajay N. Jain
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J. Comput. Aided Mol. Des. 22 (3-4) (2008)
Ajay N. Jain, Anthony Nicholls
Recommendations for evaluation of computational methods. J. Comput. Aided Mol. Des. 22 (3-4) (2008)
Tuan A. Pham, Ajay N. Jain
Customizing scoring functions for docking. J. Comput. Aided Mol. Des. 22 (5) (2008)
Ajay N. Jain
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J. Comput. Aided Mol. Des. 21 (5) (2007)
Lawrence S. Hon, Ajay N. Jain
A deterministic motif finding algorithm with application to the human genome. Bioinform. 22 (9) (2006)
Barbara A. Novak, Ajay N. Jain
Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinform. 22 (2) (2006)
Jane Fridlyand, Antoine Snijders, Dan Pinkel, Donna Albertson, Ajay N. Jain
Statistical issues in the analysis of the array CGH data. CSB (2003)
Taku A. Tokuyasu, Donna Albertson, Dan Pinkel, Ajay N. Jain
Wavelet Transforms for the Analysis of Microarray Experiments. CSB (2003)
Adam B. Olshen, Ajay N. Jain
Deriving quantitative conclusions from microarray expression data. Bioinform. 18 (7) (2002)
Ajay N. Jain
Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition. J. Comput. Aided Mol. Des. 14 (2) (2000)
Ajay N. Jain
Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comput. Aided Mol. Des. 10 (5) (1996)
Ajay N. Jain, Thomas G. Dietterich, Richard H. Lathrop, David Chapman, Roger E. Critchlow Jr., Barr E. Bauer, Teresa A. Webster, Tomás Lozano-Pérez
Compass: A shape-based machine learning tool for drug design. J. Comput. Aided Mol. Des. 8 (6) (1994)
Thomas G. Dietterich, Ajay N. Jain, Richard H. Lathrop, Tomás Lozano-Pérez
A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction. NIPS (1993)
Ajay N. Jain, Alex Waibel, David S. Touretzky
PARSEC: a structured connectionist parsing system for spoken language. ICASSP (1992)
Ajay N. Jain
Generalization Performance in PARSEC - A Structured Connectionist Parsing Architecture. NIPS (1991)
Alex Waibel, Ajay N. Jain, Arthur E. McNair, Hiroaki Saito, Alexander G. Hauptmann, Joe Tebelskis
JANUS: a speech-to-speech translation system using connectionist and symbolic processing strategies. ICASSP (1991)
Ajay N. Jain
Parsing Complex Sentences with Structured Connectionist Networks. Neural Comput. 3 (1) (1991)
Alex Waibel, Ajay N. Jain, Arthur E. McNair, Joe Tebelskis, Louise Osterholtz, Hiroaki Saito, Otto Schmidbauer, Tilo Sloboda, Monika Woszczyna
JANUS: Speech-to-Speech Translation Using Connectionist and Non-Connectionist Techniques. NIPS (1991)
Ajay N. Jain, Alexander H. Waibel
Robust connectionist parsing of spoken language. ICASSP (1990)
Ajay N. Jain, Alex Waibel
Incremental Parsing by Modular Recurrent Connectionist Networks. NIPS (1989)
Ajay N. Jain, Alex Waibel
A Connectionist Parser Aimed at Spoken Language. IWPT (1989)