NextMove Software
  • Home
  • Blog
  • News
  • Talks
  • Events
  • About Us
  • Careers
  • ELNs & Reactions
  • Patents/TextMining
  • Biologics
  • Similarity & Search
 
General Inquiries: info@nextmovesoftware.com
Support: support@nextmovesoftware.com

Publications

2024

  • Roger Sayle, "Los Alamos chess game 2 (after P-K3) is solved; Black wins in 21 moves", International Computer Games Association (ICGA) Journal, Vol 45, No. 4, pp. 92-101, 2024. Journal.

2023

  • Amanda L. Lewis, Philip Toukach, Evan Bolton, Xi Chen, Martin Frank, Thomas Lütteke, Yuriy Knirel, Ian Schoenhofen, Ajit Varki, Evgeny Vinogradov Robert J Woods, Natasha Zachara, Jian Zhang, Johannis P Kamerling, Sriram Neelamegham and the SNFG Discussion Group, "Cataloging Natural Sialic Acids and Other Nonulosonic Acids (NulOs), and their representation using the Symbol Nomenclature for Glycans", Glycobiology, January 2023. Journal.

2020

  • John J. Irwin, Khanh G. Tang, Jennifer Young, Chinzorig Dandarchuluun, Benjamin R. Wong, Munkhzul Khurelbaatar, Yurii S. Moroz, John Mayfield and Roger A. Sayle, "ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand Discovery", Journal of Chemical Information and Modeling, Vol. 60, No. 12, pp. 6065-6073, December 2020. Journal.
  • Daniel Lowe and John Mayfield, "Extraction of Reactions from Patents using Grammars", Proceedings of the CLEF 2020 Conference, CLEF 2020, September 2020. PDF.
  • CLEF 2020 Participants, "An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents", Proceedings of the CLEF 2020 Conference, CLEF 2020, September 2020. PDF.

2019

  • Sriram Neelamegham, Kiyoko Aoki-Kinoshita, Evan Bolton, Martin Frank, Frederique Lisacek, Thomas Lutteke, Noel O'Boyle, Nicolle H Packer Pamela Stanley, Philip Toukach, Ajit Varki and Robert J. Woods, "Updates to the Symbol Nomenclature for Glycans Guidelines", Glycobiology, Vol 29, No. 9, pp. 620-624, September 2019. Journal.
  • International Helminth Genomes Consortium, "Comparative Genomics of the Major Parasitic Worms", Nature Genetics, Vol. 51, No. 1, pp. 163-174, January 2019. Journal.

2018

  • Robert M. Hanson, Sophia Musachhio, John W. Mayfield, Mikko J. Vainio, Andrey Yerin and Dmitry Redkin, "Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation", Journal of Chemical Information and Modeling, Vol. 58, No. 9, pp. 1755-1765, August 2018. Journal.

2017

  • Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomas Pluskal, Miquel Rojas-Cherto, Ola Spjuth, Gilleain Torrance, Chris T. Evelo, Rajarshi Guha and Christoph Steinbeck, "The Chemistry Development Kit (CDK) v2.0: Atom Typing, Depiction, Molecular Formulas and Substructure Seaching", Journal of Cheminformatics, Vol. 9, No. 33, June 2017. Journal.
  • John W. Mayfield and Roger A. Sayle, "Technical Implications of new IUPAC Elements in Cheminformatics", Journal of Cheminformatics, Vol 9., No. 1, February 2017. Journal.
  • Peter Hunt, Matt Segall, Noel O'Boyle and Roger Sayle, "Practical Applications of Matched Series Analysis: SAR Transfer, Binding Mode Suggestion and Data Point Validation", Future Medicinal Chemistry, Vol. 9, No. 2, pp. 153-168, February 2017. Optibrium website.

2016

  • Noel M. O'Boyle and Roger A. Sayle, "Comparing Structural Fingerprints using a Literature-based Similarity Benchmark", Journal of Cheminformatics, Vol. 8, No. 36, July 2016. Journal.
  • Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Segio Martinez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W. May, Gemma L. Holliday, Christoph Steinbeck and Janet M. Thornton, "Reaction Decoder Tool (RDT): Extracting Features from Chemical Reactions", Bioinformatics, Vol. 32, No. 13, pp. 2065-2066, July 2016. Journal.
  • Nadine Schneider, Daniel M. Lowe, Roger A. Sayle, Mike A. Tarselli and Greg A. Landrum, "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter", Journal of Medicinal Chemistry, Vol. 59, No. 9, pp. 4385-4402, March 2016. Journal.
  • Daniel M. Lowe, Noel M. O'Boyle and Roger A. Sayle, "Efficient Chemical-Disease Identification and Relationship Extraction using Wikipedia to Improve Recall", Database, Vol. 2016, No. baw039, March 2016. Journal.
  • Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John May, Christoph Steinbeck and Pedro Mendes, "libChEBI: An API for Acessing the ChEBI Database", Journal of Cheminformatics, Vol. 8, No. 11, March 2016. Journal.
  • Igor V. Tetko, Daniel M. Lowe and Antony J. Williams, "The Development of Models to Predict Melting and Pyrolysis Point Data Associated with Several Hundred Thousand Compounds Mined from Patents", Journal of Cheminformatics, Vol. 8, No. 2, January 2016. Journal.

2015

  • Nadine Schneider, Roger A. Sayle and Gregory A. Landrum, "Get Your Atoms in Order - An Open-Source Implementation of a Novel and Robust Molecular Canonicalization Algorithm", Journal of Chemical Information and Modeling, Vol. 55, No. 10, pp. 2111-2120, 2015. Journal.
  • Daniel M. Lowe and Roger A. Sayle, "LeadMine: A Grammar and Dictionary Driven Approach to Entity Recognition", Journal of Cheminformatics, Vol. 7, Suppl. 1, S5, 2015. Journal
  • Nadine Scheider, Daniel M. Lowe, Roger A. Sayle and Gregory A. Landrum, "Development of a Novel Fingerprint for Chemical Reactions and Its Application to Large-Scale Reaction Classification and Similarity", Journal of Chemical Information and Modeling, Vol. 55, No. 1, pp. 39-53, 2015. Journal.
  • Noel M. O'Boyle, Roger A. Sayle and Matt Segall, "When Two Are Not Enough: Lead Optimization Beyond Matched Pairs", Drug Discovery World, pp. 55-59, Fall 2015. Journal.

2014

  • Noel M. O'Boyle, Jonas Boström, Roger A. Sayle and Adrian Gill, "Using Matched Molecular Series as a Predictive Tool to Optimize Biological Activity", Journal of Medicinal Chemistry, Vol. 57, No. 6, pp. 2704-2713, 2014. Journal.

2013

  • Daniel M. Lowe and Roger A. Sayle, "LeadMine: A Grammar and Dictionary Driven Approach to Chemical Entity Recognition", BioCreative Challenge Evaluation Workshop, Vol. 2, p. 47, October 2013.

2012

  • Roger Sayle, Paul Hongxing Xie and Sorel Muresan, "Improved Chemical Text Mining of Patents with Infinite Dictionaries and Automatic Spelling Correction", Journal of Chemical Information and Modeling (JCIM), Vol. 52, No. 1, pp. 51-62, 2012. Journal.

2010

  • Roger A. Sayle, "So You Think You Understand Tautomerism?", Journal of Computer-Aided Molecular Design (JCAMD), Vol. 24, Nos. 6-7, pp. 485-496, June 2010. Journal, PubMed.

Prior Art

  • Rachael Pirie, Harriet A. Stanway-Gordon, Hannah L. Stewart, Kirsty L. Wilson, Summer Patton, Jack Tyerman, Daniel J. Cole, Katherine Fowler and Michael J. Waring, "An Analysis of the Physicochemical Properties of Oral Drugs from 2000 to 2022", RSC Medicinal Chemistry, Vol. 15, No. 9, pp. 3125-3132, July 2024. Journal.
  • Michael Blakey, Samantha Pearman-Kanza and Jeremey G. Frey, "Zombie Cheminformatics: Extraction and Conversion of Wiswesser Line Notation (WLN) from Chemical Documents", Journal of Cheminformatics, Vol. 16, No. 42, April 2024.
  • Stuart J. Hall, Rachael Pirie and Daniel J. Cole, "Riemannian Geometry and Molecular Similarity 1: Spectrum of the Laplacian", Proceedings of the Royal Society A, Vol. 480, 20230343, 2023. Journal.
  • Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum and Daniel J. Cole, "An Open-Source Molecular Builder and Free Energy Preparation Workflow", Communications: Chemistry, Vol. 5, No. 136, October 2022. Journal.
  • John W. May and Christoph Steinbeck, "Efficient Ring Perception for the Chemistry Development Kit", Journal of Cheminformatics, Vol. 6, No. 3, January 2014. Journal.
  • Noel M. O'Boyle, Michael Banck, Craig A. James, Chirs Morley, Tim Vandermeersch and Geoffrey R. Hutchinson, "Open Babel: An Open Chemical Toolbox", Journal of Cheminformatics, Vol. 3, No. 33, October 2011. Journal.
  • Daniel M. Lowe, Peter D. Corbett, Peter Murray-Rust and Robert C. Glen, "Chemical Name to Structure: OPSIN, an Open Source Solution", Journal of Chemical Information and Modeling (JCIM), Vol. 51, No. 3, pp. 739-753, March 2011. Journal.
  • Roger Sayle, "Preserving Nuance in Chemical Nomenclature Translation", The ATA Chronicle (The Journal of the American Translators Association), October 2009.
  • Roger Sayle, "Foreign Language Translation of Chemical Nomenclature by Computer", Journal of Chemical Information and Modeling (JCIM), Vol. 49, No. 3, pp. 519-530, February 2009. Journal.
  • Roger Anthony Sayle, "A Superoptimizer Analysis of Multiway Branch Code Generation", Proceedings of the 2008 GCC Developers' Summit, Ottawa, Canada, 17-19 June 2008. PDF.
  • Roger Sayle and Anthony Nicholls, "Electrostatic Evaluation of Isosteric Analogues", Journal of Computer-Aided Molecular Design (JCAMD), Vol. 20, No. 4, pp. 191-208, July 2006. Journal.
  • J. Andrew Grant, James A. Haigh, Barry T. Pickup, Anthony Nicholls and Roger A. Sayle, "Lingos, Finite State Machines and Fast Similarity", Journal of Chemical Information and Modeling (JCIM), Vol. 46, No. 5, pp. 1912-1918, 2006. Journal.
  • Gary Hurd, "Free For All: Roger Sayle collects the Heatley Medal", The Biochemist, pp. 29-31, 2000.
  • S. Taylor, T.C. Hodgman, C.H. O'Donnell, C.B. Littler, R.A. Sayle, R.W. Gill and A. Lyall, "Automated Management of Gene Discovery Projects using a Hierarchical Automated Gene Identification System (HAGIS)", Bioinformatics, Vol. 14, No. 2, pp. 217-218, March 1998.
  • Robert B. Russell, Mansoor A. Saqi, Paul A. Bates, Roger A. Sayle and Michael J.E. Sternberg, "Recognition of Analogous and Homologous Protein Folds: Assessment of Prediction Success and Associated Alignment Accuracy using Empirical Substitution Matrices", Protein Engineering, Vol. 11, No. 1, pp. 1-9, 1998.
  • Robert B. Russell, Mansoor A. Saqi, Roger A. Sayle, Paul A. Bates and Michael J.E. Sternberg, "Recognition of Analogous and Homologous Protein Folds: Analysis of Sequence and Structure Conservation", Journal of Molecular Biology (JMB), Vol. 269, pp. 423-439, 1997.
  • Roger Sayle and E. James Milner-White, "RasMol: Biomolecular Graphics for All", Trends in Biochemical Sciences (TIBS), Vol. 20, No. 9, pp. 333-379, September 1995.
Arthor provides fast state-of-the-art substructure and chemical similarity search capabilities for ultra-large databases of hundreds of millions of compounds, using SMARTS optimization, Just-In-Time compilation and/or GPUs.
CaffeineFix is used to rapidly match chemical names or terms against a dictionary or grammar (e.g. a grammar for IUPAC names). As well as use in text-mining, it can be used to provide autocomplete functionality and spell-correction.
Casandra is a server for delivering real time safety warnings of experimental hazards straight to the pharmaceutical electronic laboratory notebooks (ELNs).
HazELNut is a suite of tools used to extract, normalize and analyse information in Electronic Lab Notebooks (ELNs). This can be used to implement a search interface, find/eliminate duplicates, find similar reactions and so on.
LeadMine extracts chemical names and terms from text. It incorporates NextMove's CaffeineFix technology to find terms that match appropriate dictionaries or grammars. It has enhanced functionality to handle the patent literature.
Matsy is a set of tools for creating and analysing Matched Molecular Series (the general form of Matched Molecular Pairs). In particular, it can be used to suggest what compound to make next in a Medicinal Chemistry program.
MPSearch rapidly searches a database to find Matched Pairs related to a query molecule. This type of search is used to explore previous medicinal chemistry strategies.
NameRXN is used to classify and name reactions. It is particular useful in the context of ELN analysis but also as a plugin to chemical drawing software. NameRXN builds on NextMove Software's Patsy technology.
Patsy is used to speed up SMARTS pattern matching by creating optimized SMARTS patterns or source code. Speed gains are particularly large when multiple SMARTS patterns are matched against a single structure.
Pistachio is a reaction dataset browser providing loading, querying, and analytics of chemical reactions. With over 21 million chemical reactions extracted from US & EPO patents, it demonstrates an AI interface to faceted (structure) search
SmallWorld is an index of chemical space based on more than 230 billion molecular substructures. It can be used to measure similarity based on graph-edit distance, find the MCS of two or more molecules, analyse HTS results and much more.
Sugar & Splice can be used to perceive and depict biopolymer structure. It makes it easy to interconvert between small-molecule representations (e.g. SMILES, MOL) and biopolymer representations (HELM, IUPAC line notation).
©2025 NextMove Software. All rights reserved.