{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,29]],"date-time":"2025-11-29T10:59:46Z","timestamp":1764413986575,"version":"3.37.3"},"reference-count":93,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T00:00:00Z","timestamp":1690502400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T00:00:00Z","timestamp":1690502400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Molecular descriptors characterize the biological, physical, and chemical properties of molecules and have long been used for understanding molecular interactions and facilitating materials design. Some of the most robust descriptors are derived from geometrical representations of molecules, called 3-dimensional (3D) descriptors. When calculated from molecular dynamics (MD) simulation trajectories, 3D descriptors can also capture the effects of operating conditions such as temperature or pressure. However, extracting 3D descriptors from MD trajectories is non-trivial, which hinders their wide use by researchers developing advanced quantitative-structure\u2013property-relationship models using machine learning. Here, we describe a suite of open-source Python-based post-processing routines, called PyL3dMD, for calculating 3D descriptors from MD simulations. PyL3dMD is compatible with the popular simulation package LAMMPS and enables users to compute more than 2000 3D molecular descriptors from atomic trajectories generated by MD simulations. PyL3dMD is freely available via GitHub and can be easily installed and used as a highly flexible Python package on all major platforms (Windows, Linux, and macOS). A performance benchmark study used descriptors calculated by PyL3dMD to develop a neural network and the results showed that PyL3dMD is fast and efficient in calculating descriptors for large and complex molecular systems with long simulation durations. PyL3dMD facilitates the calculation of 3D molecular descriptors using MD simulations, making it a valuable tool for cheminformatics studies.<\/jats:p><jats:p><jats:bold>Graphical Abstract<\/jats:bold><\/jats:p>","DOI":"10.1186\/s13321-023-00737-5","type":"journal-article","created":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T15:01:52Z","timestamp":1690556512000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["PyL3dMD: Python LAMMPS 3D molecular descriptors package"],"prefix":"10.1186","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5859-3927","authenticated-orcid":false,"given":"Pawan","family":"Panwar","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4395-9866","authenticated-orcid":false,"given":"Quanpeng","family":"Yang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2017-6081","authenticated-orcid":false,"given":"Ashlie","family":"Martini","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,7,28]]},"reference":[{"key":"737_CR1","doi-asserted-by":"publisher","DOI":"10.1007\/s00894-019-4011-x","author":"H Ch\u00e1vez Thielemann","year":"2019","unstructured":"Ch\u00e1vez Thielemann H, Cardellini A, Fasano M, Bergamasco L, Alberghini M, Ciorra G, Chiavazzo E, Asinari P (2019) From GROMACS to LAMMPS: GRO2LAM: A Converter for Molecular Dynamics Software. J Mol Model. https:\/\/doi.org\/10.1007\/s00894-019-4011-x","journal-title":"J Mol Model"},{"key":"737_CR2","unstructured":"Plimpton S, et al (2007) LAMMPS-large-scale atomic\/molecular massively parallel simulator. Sandia National Laboratories."},{"key":"737_CR3","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2021.108171","volume":"271","author":"AP Thompson","year":"2022","unstructured":"Thompson AP, Aktulga HM, Berger R, Bolintineanu DS, Brown WM, Crozier PS et al (2022) LAMMPS\u2014a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput Phys Commun 271:108171","journal-title":"Comput Phys Commun"},{"key":"737_CR4","doi-asserted-by":"crossref","unstructured":"David A, Pearlman A, David A (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun","DOI":"10.1016\/0010-4655(95)00041-D"},{"issue":"7","key":"737_CR5","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","volume":"29","author":"S Pronk","year":"2013","unstructured":"Pronk S, P\u00e1ll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, Van Der Spoel D, Hess B, Lindahl E (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29(7):845\u2013854","journal-title":"Bioinformatics"},{"issue":"10","key":"737_CR6","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks","year":"2009","unstructured":"Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545\u20131614","journal-title":"J Comput Chem"},{"issue":"24","key":"737_CR7","doi-asserted-by":"publisher","first-page":"9181","DOI":"10.1021\/ja202726y","volume":"133","author":"Y Shan","year":"2011","unstructured":"Shan Y, Kim ET, Eastwood MP, Dror RO, Seeliger MA, Shaw DE (2011) How does a drug molecule find its target binding site? J Am Chem Soc 133(24):9181\u20139183","journal-title":"J Am Chem Soc"},{"key":"737_CR8","volume-title":"Materials studio","author":"Biovia, and Dassault Syst\u00e8mes","year":"2020","unstructured":"Biovia, and Dassault Syst\u00e8mes (2020) Materials studio. Dassault Syst\u00e8mes, San Diego"},{"key":"737_CR9","unstructured":"Phillips JC, Schulten K, Bhatele A, Mei C, Sun Y, Bohm EJ, Kale LV (2016) Scalable molecular dynamics with NAMD, parallel science and engineering applications: the Charm++ approach, pp 60\u201376."},{"issue":"1","key":"737_CR10","doi-asserted-by":"publisher","first-page":"015901","DOI":"10.1088\/1361-648X\/ab4007","volume":"32","author":"S Smidstrup","year":"2020","unstructured":"Smidstrup S, Markussen T, Vancraeyveld P, Wellendorff J, Schneider J, Gunst T, Verstichel B, Stradi D, Khomyakov PA, Vej-Hansen UG, Lee ME, Chill ST, Rasmussen F, Penazzi G, Corsetti F, Ojanper\u00e4 A, Jensen K, Palsgaard MLN, Martinez U, Blom A, Brandbyge M, Stokbro K (2020) QuantumATK: an integrated platform of electronic and atomic-scale modelling tools. J Phys Condens Matter 32(1):015901","journal-title":"J Phys Condens Matter"},{"key":"737_CR11","unstructured":"Dias CS (2021) Molecular dynamics simulations of active matter using LAMMPS."},{"key":"737_CR12","unstructured":"Leszczynski J (2010) Recent advances in QSAR studies."},{"key":"737_CR13","doi-asserted-by":"crossref","unstructured":"Todeschini R, Consonni V (2010) Molecular descriptors for chemoinformatics.","DOI":"10.1002\/9783527628766"},{"key":"737_CR14","doi-asserted-by":"publisher","unstructured":"Dehmer M, Varmuza K, Bonchev D (2012) Statistical modelling of molecular descriptors in QSAR\/QSPR. https:\/\/doi.org\/10.1002\/9783527645121","DOI":"10.1002\/9783527645121"},{"key":"737_CR15","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-018-0258-y","author":"H Moriwaki","year":"2018","unstructured":"Moriwaki H, Tian YS, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. J Cheminform. https:\/\/doi.org\/10.1186\/s13321-018-0258-y","journal-title":"J Cheminform."},{"key":"737_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-015-0109-z","author":"J Dong","year":"2015","unstructured":"Dong J, Cao DS, Miao HY, Liu S, Deng BC, Yun YH, Wang NN, Lu AP, Zeng WB, Chen AF (2015) ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation. J Cheminform. https:\/\/doi.org\/10.1186\/s13321-015-0109-z","journal-title":"J Cheminform."},{"issue":"2","key":"737_CR17","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/S1461-5347(99)00215-1","volume":"3","author":"M Grover","year":"2000","unstructured":"Grover M, Singh B, Bakshi M, Singh S (2000) Quantitative structure-property relationships in pharmaceutical research\u2013part 1. Pharm Sci Technolo Today 3(2):50\u201357","journal-title":"Pharm Sci Technolo Today"},{"issue":"2","key":"737_CR18","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/S1461-5347(99)00215-1","volume":"3","author":"M Grover","year":"2000","unstructured":"Grover M, Singh B, Bakshi M, Singh S (2000) Quantitative structure-property relationships in pharmaceutical research\u2014part 2. Pharm Sci Technolo Today 3(2):50\u201357","journal-title":"Pharm Sci Technolo Today"},{"issue":"7","key":"737_CR19","doi-asserted-by":"publisher","first-page":"2585","DOI":"10.1021\/cr940024m","volume":"102","author":"CD Selassie","year":"2002","unstructured":"Selassie CD, Garg R, Kapur S, Kurup A, Verma RP, Mekapati SB, Hansch C (2002) Comparative QSAR and the radical toxicity of various functional groups. Chem Rev 102(7):2585\u20132605","journal-title":"Chem Rev"},{"issue":"10","key":"737_CR20","doi-asserted-by":"publisher","first-page":"5714","DOI":"10.1021\/cr900238d","volume":"110","author":"AR Katritzky","year":"2010","unstructured":"Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA (2010) Quantitative correlation of physical and chemical properties with chemical structure: utility for prediction. Chem Rev 110(10):5714\u20135789","journal-title":"Chem Rev"},{"issue":"119215","key":"737_CR21","doi-asserted-by":"publisher","DOI":"10.1016\/j.molliq.2022.119215","volume":"359","author":"P Panwar","year":"2022","unstructured":"Panwar P, Schweissinger E, Maier S, Hilf S, Sirak S, Martini A (2022) Effect of polymer structure and chemistry on viscosity index, thickening efficiency, and traction coefficient of lubricants. J Mol Liq 359(119215):119215","journal-title":"J Mol Liq"},{"key":"737_CR22","unstructured":"John D, Andrew W (2007) In silico prediction of physicochemical properties, Luxembourg."},{"issue":"4","key":"737_CR23","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1080\/1062936X.2013.773372","volume":"24","author":"JC Dearden","year":"2013","unstructured":"Dearden JC, Rotureau P, Fayet G (2013) QSPR prediction of physico-chemical properties for REACH. SAR QSAR Environ Res 24(4):279\u2013318","journal-title":"SAR QSAR Environ Res"},{"issue":"2","key":"737_CR24","first-page":"237","volume":"56","author":"A Mauri","year":"2006","unstructured":"Mauri A, Consonni V, Pavan M, Todeschini R (2006) DRAGON software: an easy approach to molecular descriptor calculations. Match 56(2):237\u2013248","journal-title":"Match"},{"issue":"3","key":"737_CR25","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1021\/ci015504a","volume":"42","author":"V Consonni","year":"2002","unstructured":"Consonni V, Todeschini R, Pavan M (2002) Structure\/response correlations and similarity\/diversity analysis by GETAWAY descriptors. 1. Theory of the novel 3D molecular descriptors. J Chem Inf Comput Sci 42(3):682\u2013692","journal-title":"J Chem Inf Comput Sci"},{"issue":"7","key":"737_CR26","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1002\/jcc.21707","volume":"32","author":"CW Yap","year":"2010","unstructured":"Yap CW (2010) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32(7):1466\u20131474","journal-title":"J Comput Chem"},{"key":"737_CR27","volume-title":"Blue-desc descriptor calculator","author":"H Georg","year":"2008","unstructured":"Georg H (2008) Blue-desc descriptor calculator. University of T\u00fcbingen, T\u00fcbingen"},{"key":"737_CR28","unstructured":"Landrum G (2011) RDKit : a software suite for cheminformatics , computational chemistry , and predictive modelling. Components."},{"key":"737_CR29","doi-asserted-by":"publisher","DOI":"10.1002\/chin.200321205","author":"C Steinbeck","year":"2003","unstructured":"Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E (2003) The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. ChemInform. https:\/\/doi.org\/10.1002\/chin.200321205","journal-title":"ChemInform"},{"key":"737_CR30","doi-asserted-by":"publisher","DOI":"10.1186\/1752-153X-2-24","author":"NM O\u2019Boyle","year":"2008","unstructured":"O\u2019Boyle NM, Hutchison GR (2008) Cinfony\u2014combining open source cheminformatics toolkits behind a common interface. Chem Cent J. https:\/\/doi.org\/10.1186\/1752-153X-2-24","journal-title":"Chem Cent J"},{"issue":"8","key":"737_CR31","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1093\/bioinformatics\/btt105","volume":"29","author":"DS Cao","year":"2013","unstructured":"Cao DS, Xu QS, Hu QN, Liang YZ (2013) ChemoPy: freely available python package for computational biology and chemoinformatics. Bioinformatics 29(8):1092\u20131094","journal-title":"Bioinformatics"},{"issue":"18","key":"737_CR32","doi-asserted-by":"publisher","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","volume":"24","author":"RCG Holland","year":"2008","unstructured":"Holland RCG, Down TA, Pocock M, Prli\u0107 A, Huen D, James K, Foisy S, Dr\u00e4ger A, Yates A, Heuer M, Schreiber MJ (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics 24(18):2096\u20132097","journal-title":"Bioinformatics"},{"issue":"1","key":"737_CR33","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s13321-016-0146-2","volume":"8","author":"J Dong","year":"2016","unstructured":"Dong J, Yao ZJ, Wen M, Zhu MF, Wang NN, Miao HY, Lu AP, Zeng WB, Cao DS (2016) BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs\/RNAs and their interactions. J. Cheminform. 8(1):34","journal-title":"J. Cheminform."},{"key":"737_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-59","author":"O Spjuth","year":"2007","unstructured":"Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES (2007) Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics. https:\/\/doi.org\/10.1186\/1471-2105-8-59","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"737_CR35","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1093\/bioinformatics\/btt072","volume":"29","author":"DS Cao","year":"2013","unstructured":"Cao DS, Xu QS, Liang YZ (2013) Propy: a tool to generate various modes of Chou\u2019s PseAAC. Bioinformatics 29(7):960\u2013962","journal-title":"Bioinformatics"},{"issue":"11","key":"737_CR36","doi-asserted-by":"publisher","first-page":"3086","DOI":"10.1021\/ci400127q","volume":"53","author":"DS Cao","year":"2013","unstructured":"Cao DS, Liang YZ, Yan J, Tan GS, Xu QS, Liu S (2013) PyDPI: freely available python package for chemoinformatics, bioinformatics, and chemogenomics studies. J Chem Inf Model 53(11):3086\u20133096","journal-title":"J Chem Inf Model"},{"issue":"8","key":"737_CR37","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/bioinformatics\/btu820","volume":"31","author":"B Liu","year":"2015","unstructured":"Liu B, Liu F, Fang L, Wang X, Chou KC (2015) RepDNA: a python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects. Bioinformatics 31(8):1307\u20131309","journal-title":"Bioinformatics"},{"key":"737_CR38","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-159","author":"T Kuhn","year":"2010","unstructured":"Kuhn T, Willighagen EL, Zielesny A, Steinbeck C (2010) CDK-taverna: an open workflow environment for cheminformatics. BMC Bioinformatics. https:\/\/doi.org\/10.1186\/1471-2105-11-159","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"737_CR39","doi-asserted-by":"publisher","first-page":"1857","DOI":"10.1093\/bioinformatics\/btv042","volume":"31","author":"N Xiao","year":"2015","unstructured":"Xiao N, Cao DS, Zhu MF, Xu QS (2015) Protr\/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics 31(11):1857\u20131859","journal-title":"Bioinformatics"},{"key":"737_CR40","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-3-3","author":"G Hinselmann","year":"2011","unstructured":"Hinselmann G, Rosenbaum L, Jahn A, Fechner N, Zell A (2011) JCompoundMapper: an open source java library and command-line tool for chemical fingerprints. J Cheminform. https:\/\/doi.org\/10.1186\/1758-2946-3-3","journal-title":"J. Cheminform."},{"issue":"15","key":"737_CR41","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1093\/bioinformatics\/btn307","volume":"24","author":"Y Cao","year":"2008","unstructured":"Cao Y, Charisi A, Cheng LC, Jiang T, Girke T (2008) ChemmineR: a compound mining framework for R. Bioinformatics 24(15):1733\u20131734","journal-title":"Bioinformatics"},{"issue":"2","key":"737_CR42","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1093\/bioinformatics\/btu624","volume":"31","author":"DS Cao","year":"2015","unstructured":"Cao DS, Xiao N, Xu QS, Chen AF (2015) Rcpi: R\/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. Bioinformatics 31(2):279\u2013281","journal-title":"Bioinformatics"},{"issue":"1","key":"737_CR43","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1021\/ci00057a005","volume":"28","author":"D Weininger","year":"1988","unstructured":"Weininger D (1988) SMILES, a chemical language and information system: 1: introduction to methodology and encoding rules. J Chem Inf Comput Sci 28(1):31\u201336","journal-title":"J Chem Inf Comput Sci"},{"issue":"4","key":"737_CR44","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1021\/ci00004a014","volume":"31","author":"AT Balaban","year":"1991","unstructured":"Balaban AT, Ciubotariu D, Medeleanu M (1991) Topological indices and real number vertex invariants based on graph eigenvalues or eigenvectors. J Chem Inf Comput Sci 31(4):517\u2013523","journal-title":"J Chem Inf Comput Sci"},{"issue":"6","key":"737_CR45","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1002\/jps.2600700602","volume":"70","author":"LB Kier","year":"1981","unstructured":"Kier LB, Hall LH (1981) Derivation and significance of valence molecular connectivity. J Pharm Sci 70(6):583\u2013589","journal-title":"J Pharm Sci"},{"issue":"2","key":"737_CR46","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1021\/ci960049h","volume":"37","author":"V Sharma","year":"1997","unstructured":"Sharma V, Goswami R, Madan AK (1997) Eccentric connectivity index: a novel highly discriminating topological descriptor for structure\u2212property and structure\u2212activity studies. J Chem Inf Comput Sci 37(2):273\u2013282","journal-title":"J Chem Inf Comput Sci"},{"issue":"23","key":"737_CR47","doi-asserted-by":"publisher","first-page":"6609","DOI":"10.1021\/ja00856a001","volume":"97","author":"M Randic","year":"1975","unstructured":"Randic M (1975) Characterization of molecular branching. J Am Chem Soc 97(23):6609\u20136615","journal-title":"J Am Chem Soc"},{"issue":"1","key":"737_CR48","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/S1093-3263(01)00098-5","volume":"20","author":"M Randi\u0107","year":"2001","unstructured":"Randi\u0107 M (2001) The connectivity index 25 years after. J Mol Graph Model 20(1):19\u201335","journal-title":"J Mol Graph Model"},{"issue":"12","key":"737_CR49","doi-asserted-by":"publisher","first-page":"1743","DOI":"10.1002\/jps.2600671229","volume":"67","author":"LH Hall","year":"1978","unstructured":"Hall LH, Kier LB (1978) Molecular connectivity and substructure analysis. J Pharm Sci 67(12):1743\u20131747","journal-title":"J Pharm Sci"},{"key":"737_CR50","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1002\/9780470125793.ch9","volume":"2","author":"LH Hall","year":"2007","unstructured":"Hall LH, Kier LB (2007) The molecular connectivity chi indexes and kappa shape indexes in structure-property modeling. Rev Comput Chem 2:367\u2013422","journal-title":"Rev Comput Chem"},{"issue":"1","key":"737_CR51","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/BF01164642","volume":"12","author":"O Ivanciuc","year":"1993","unstructured":"Ivanciuc O, Balaban T-S, Balaban AT (1993) Design of topological indices. Part 4. Reciprocal distance matrix, related local vertex invariants and topological indices. J Math Chem 12(1):309\u2013318","journal-title":"J Math Chem"},{"issue":"1","key":"737_CR52","first-page":"83","volume":"50","author":"I Gutman","year":"2004","unstructured":"Gutman I, Das KC (2004) The first zagreb index 30 years after. MATCH Commun Math Comput Chem 50(1):83\u201392","journal-title":"MATCH Commun Math Comput Chem"},{"issue":"3","key":"737_CR53","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1021\/cr950202r","volume":"96","author":"M Karelson","year":"1996","unstructured":"Karelson M, Lobanov VS, Katritzky AR (1996) Quantum-chemical descriptors in QSAR\/QSPR studies. Chem Rev 96(3):1027\u20131044","journal-title":"Chem Rev"},{"issue":"5","key":"737_CR54","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1021\/ci970424l","volume":"37","author":"DD Robinson","year":"1997","unstructured":"Robinson DD, Barlow TW, Richards WG (1997) Reduced dimensional representations of molecular structure. J Chem Inf Comput Sci 37(5):939\u2013942","journal-title":"J Chem Inf Comput Sci"},{"key":"737_CR55","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1002\/9780470125861.ch5","volume-title":"Molecular shape descriptors, Reviews in computational chemistry","author":"GA Arteca","year":"2007","unstructured":"Arteca GA (2007) Molecular shape descriptors, Reviews in computational chemistry. John Wiley & Sons Inc, Hoboken, pp 191\u2013253"},{"issue":"24","key":"737_CR56","doi-asserted-by":"publisher","first-page":"10400","DOI":"10.1021\/jp953224q","volume":"100","author":"AR Katritzky","year":"1996","unstructured":"Katritzky AR, Mu L, Lobanov VS, Karelson M (1996) Correlation of boiling points with molecular structure. 1. A training set of 298 diverse organics and a test set of 9 simple inorganics. J Phys Chem 100(24):10400\u201310407","journal-title":"J Phys Chem"},{"issue":"19","key":"737_CR57","doi-asserted-by":"publisher","first-page":"7368","DOI":"10.1021\/jo034808o","volume":"68","author":"YH Zhao","year":"2003","unstructured":"Zhao YH, Abraham MH, Zissimos AM (2003) Fast calculation of van der Waals volume as a sum of atomic and bond contributions and its application to drug compounds. J Org Chem 68(19):7368\u20137373","journal-title":"J Org Chem"},{"issue":"10","key":"737_CR58","doi-asserted-by":"publisher","first-page":"2516","DOI":"10.1021\/ci300293f","volume":"52","author":"NC Firth","year":"2012","unstructured":"Firth NC, Brown N, Blagg J (2012) Plane of best fit: a novel method to characterize the three-dimensionality of molecules. J Chem Inf Model 52(10):2516\u20132525","journal-title":"J Chem Inf Model"},{"issue":"1","key":"737_CR59","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1021\/ja01193a005","volume":"69","author":"H Wiener","year":"1947","unstructured":"Wiener H (1947) Structural determination of paraffin boiling points. J Am Chem Soc 69(1):17\u201320","journal-title":"J Am Chem Soc"},{"issue":"3","key":"737_CR60","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1021\/ci00025a005","volume":"35","author":"M Randic","year":"1995","unstructured":"Randic M (1995) Molecular shape profiles. J Chem Inf Comput Sci 35(3):373\u2013382","journal-title":"J Chem Inf Comput Sci"},{"issue":"2","key":"737_CR61","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1021\/ci00018a008","volume":"34","author":"M Randic","year":"1994","unstructured":"Randic M, Kleiner AF, De Alba LM (1994) Distance\/distance matrixes. J Chem Inf Comput Sci 34(2):277\u2013286","journal-title":"J Chem Inf Comput Sci"},{"issue":"6","key":"737_CR62","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1002\/(SICI)1097-461X(1999)75:6<1017::AID-QUA6>3.0.CO;2-C","volume":"75","author":"M Randi","year":"1999","unstructured":"Randi M, Krilov G (1999) On a characterization of the folding of proteins. Int J Quantum Chem 75(6):1017\u20131026","journal-title":"Int J Quantum Chem"},{"issue":"3","key":"737_CR63","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1007\/BF01169597","volume":"3","author":"B Bogdanov","year":"1989","unstructured":"Bogdanov B, Nikoli\u0107 S, Trinajsti\u0107 N (1989) On the three-dimensional wiener number. J Math Chem 3(3):299\u2013309","journal-title":"J Math Chem"},{"issue":"1","key":"737_CR64","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/0009-2614(91)90285-H","volume":"179","author":"S Nikoli\u0107","year":"1991","unstructured":"Nikoli\u0107 S, Trinajsti\u0107 N, Mihali\u0107 Z, Carter S (1991) On the geometric-distance matrix and the corresponding structural invariants of molecular systems. Chem Phys Lett 179(1):21\u201328","journal-title":"Chem Phys Lett"},{"issue":"4","key":"737_CR65","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1021\/ci00008a012","volume":"32","author":"M Petitjean","year":"1992","unstructured":"Petitjean M (1992) Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds. J Chem Inf Comput Sci 32(4):331\u2013337","journal-title":"J Chem Inf Comput Sci"},{"issue":"4","key":"737_CR66","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1021\/ci00026a007","volume":"35","author":"PA Bath","year":"1995","unstructured":"Bath PA, Poirrette AR, Willett P, Allen FH (1995) The extent of the relationship between the graph-theoretical and the geometrical shape coefficients of chemical compounds. J Chem Inf Comput Sci 35(4):714\u2013716","journal-title":"J Chem Inf Comput Sci"},{"issue":"4","key":"737_CR67","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1002\/jcc.540070419","volume":"7","author":"AK Ghose","year":"1986","unstructured":"Ghose AK, Crippen GM (1986) Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships I. Partition coefficients as a measure of hydrophobicity. J Comput Chem 7(4):565\u2013577","journal-title":"J Comput Chem"},{"issue":"3","key":"737_CR68","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1021\/ci0155053","volume":"42","author":"V Consonni","year":"2002","unstructured":"Consonni V, Todeschini R, Pavan M, Gramatica P (2002) Structure\/response correlations and similarity\/diversity analysis by GETAWAY descriptors. 2. Application of the novel 3D molecular descriptors to QSAR\/QSPR studies. J Chem Inf Comput Sci 42(3):693\u2013705","journal-title":"J Chem Inf Comput Sci"},{"issue":"21","key":"737_CR69","doi-asserted-by":"publisher","first-page":"2323","DOI":"10.1021\/ac00220a013","volume":"62","author":"DT Stanton","year":"1990","unstructured":"Stanton DT, Jurs PC (1990) Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Anal Chem 62(21):2323\u20132329","journal-title":"Anal Chem"},{"issue":"20","key":"737_CR70","doi-asserted-by":"publisher","first-page":"3714","DOI":"10.1021\/jm000942e","volume":"43","author":"P Ertl","year":"2000","unstructured":"Ertl P, Rohde B, Selzer P (2000) Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J Med Chem 43(20):3714\u20133717","journal-title":"J Med Chem"},{"key":"737_CR71","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1023\/A:1027284627085","volume":"9\u201311","author":"R Todeschini","year":"1998","unstructured":"Todeschini R, Gramatica P (1998) New 3D molecular descriptors: the WHIM theory and QSAR applications. Perspect Drug Discov Des 9\u201311:355\u2013380","journal-title":"Perspect Drug Discov Des"},{"issue":"1\u20134","key":"737_CR72","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1080\/10629369708039126","volume":"7","author":"R Todeschini","year":"1997","unstructured":"Todeschini R, Gramatica P (1997) The whim theory: new 3D molecular descriptors for QSAR in environmental modelling. SAR QSAR Environ Res 7(1\u20134):89\u2013115","journal-title":"SAR QSAR Environ Res"},{"issue":"2","key":"737_CR73","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1002\/qsar.19970160204","volume":"16","author":"R Todeschini","year":"1997","unstructured":"Todeschini R, Gramatica P (1997) 3D-modelling and prediction by WHIM descriptors. Part 6. Application of WHIM descriptors in QSAR studies. Quant Struct-Act Relat 16(2):120\u2013125","journal-title":"Quant Struct-Act Relat"},{"issue":"4","key":"737_CR74","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1002\/cem.1180080405","volume":"8","author":"R Todeschini","year":"1994","unstructured":"Todeschini R, Lasagni M, Marengo E (1994) New molecular descriptors for 2D and 3D structures. Theory J Chemom 8(4):263\u2013272","journal-title":"Theory J Chemom"},{"issue":"1","key":"737_CR75","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/S0924-2031(99)00014-4","volume":"19","author":"MC Hemmer","year":"1999","unstructured":"Hemmer MC, Steinhauer V, Gasteiger J (1999) Deriving the 3D structure of organic molecules from their infrared spectra. Vib Spectrosc 19(1):151\u2013164","journal-title":"Vib Spectrosc"},{"issue":"2","key":"737_CR76","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1021\/ci950164c","volume":"36","author":"JH Schuur","year":"1996","unstructured":"Schuur JH, Selzer P, Gasteiger J (1996) The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. J Chem Inf Comput Sci 36(2):334\u2013344","journal-title":"J Chem Inf Comput Sci"},{"key":"737_CR77","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.jmgm.2014.10.006","volume":"54","author":"O Devinyak","year":"2014","unstructured":"Devinyak O, Havrylyuk D, Lesyk R (2014) 3D-MoRSE descriptors explained. J Mol Graph Model 54:194\u2013203","journal-title":"J Mol Graph Model"},{"issue":"1","key":"737_CR78","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1021\/ci0256236","volume":"44","author":"CT Klein","year":"2004","unstructured":"Klein CT, Kaiser D, Ecker G (2004) Topological distance based 3D descriptors for use in QSAR and diversity analysis. J Chem Inf Comput Sci 44(1):200\u2013209","journal-title":"J Chem Inf Comput Sci"},{"issue":"2","key":"737_CR79","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1021\/ef020200r","volume":"17","author":"E Rogel","year":"2003","unstructured":"Rogel E, Carbognani L (2003) Density estimation of asphaltenes using molecular dynamics simulations. Energy Fuels 17(2):378\u2013386","journal-title":"Energy Fuels"},{"key":"737_CR80","doi-asserted-by":"crossref","unstructured":"Todeschini R, Consonni V (2000) Handbook of molecular descriptors.","DOI":"10.1002\/9783527613106"},{"issue":"4","key":"737_CR81","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1021\/ci00020a020","volume":"33","author":"D Rogers","year":"1993","unstructured":"Rogers D, Hopfinger AJ (1993) Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships. J Chem Inf Comput Sci 33(4):854\u2013866","journal-title":"J Chem Inf Comput Sci"},{"issue":"5","key":"737_CR82","doi-asserted-by":"publisher","first-page":"2030","DOI":"10.1021\/ci060104e","volume":"46","author":"L Bernazzani","year":"2006","unstructured":"Bernazzani L, Duce C, Micheli A, Mollica V, Sperduti A, Starita A, Tin\u00e9 MR (2006) Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks. J Chem Inf Model 46(5):2030\u20132042","journal-title":"J Chem Inf Model"},{"issue":"6","key":"737_CR83","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1021\/ci9903298","volume":"39","author":"M Cocchi","year":"1999","unstructured":"Cocchi M, De Benedetti PG, Seeber R, Tassi L, Ulrici A (1999) Development of quantitative structure-property relationships using calculated descriptors for the prediction of the physicochemical properties (ND, \u03c1, Bp, \u2208, \u03b7) of a series of organic solvents. J Chem Inf Comput Sci 39(6):1190\u20131203","journal-title":"J Chem Inf Comput Sci"},{"issue":"3","key":"737_CR84","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1021\/ci980117v","volume":"39","author":"O Ivanciuc","year":"1999","unstructured":"Ivanciuc O, Ivanciuc T, Filip PA, Cabrol-Bass D (1999) Estimation of the liquid viscosity of organic compounds with a quantitative structure\u2212property model. J Chem Inf Comput Sci 39(3):515\u2013524","journal-title":"J Chem Inf Comput Sci"},{"key":"737_CR85","doi-asserted-by":"crossref","unstructured":"Lam SK, Pitrou A, Seibert S (2015) Numba: A LLVM-Based Python JIT Compiler. Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC, Association for Computing Machinery, New York, NY, USA, pp 1\u20136.","DOI":"10.1145\/2833157.2833162"},{"issue":"45","key":"737_CR86","doi-asserted-by":"publisher","first-page":"11225","DOI":"10.1021\/ja9621760","volume":"118","author":"WL Jorgensen","year":"1996","unstructured":"Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118(45):11225\u201311236","journal-title":"J Am Chem Soc"},{"issue":"1","key":"737_CR87","first-page":"31","volume":"4","author":"P Dauber-Osguthorpe","year":"1988","unstructured":"Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT (1988) \u201cStructure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system\u201d, proteins: structure. Function, and Genetics 4(1):31\u201347","journal-title":"Function, and Genetics"},{"issue":"1\u20133","key":"737_CR88","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1080\/08927022.2013.842994","volume":"40","author":"BL Eggimann","year":"2014","unstructured":"Eggimann BL, Sunnarborg AJ, Stern HD, Bliss AP, Siepmann JI (2014) An online parameter and property database for the TraPPE force field. Mol Simul 40(1\u20133):101\u2013105","journal-title":"Mol Simul"},{"issue":"1","key":"737_CR89","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/npjcompumats.2015.11","volume":"2","author":"TP Senftle","year":"2016","unstructured":"Senftle TP, Hong S, Islam MM, Kylasa SB, Zheng Y, Shin YK, Junkermeier C, Engel-Herbert R, Janik MJ, Aktulga HM, Verstraelen T, Grama A, van Duin ACT (2016) The ReaxFF reactive force-field: development, applications and future directions. NPJ Comput Mater 2(1):1\u201314","journal-title":"NPJ Comput Mater"},{"key":"737_CR90","volume-title":"Properties of hydrocarbons of high molecular weight synthesized by research project 42 of the American Petroleum Institute","author":"American Petroleum Institute","year":"1967","unstructured":"American Petroleum Institute (1967) Properties of hydrocarbons of high molecular weight synthesized by research project 42 of the American Petroleum Institute. American Petroleum Institute, New York"},{"key":"737_CR91","doi-asserted-by":"crossref","unstructured":"Panwar P, Yang Q, Martini A (2023) Temperature-dependent density and viscosity prediction for hydrocarbons: machine learning and molecular dynamics simulations. J Chem Inf Model.","DOI":"10.1021\/acs.jcim.3c00231"},{"issue":"W1","key":"737_CR92","doi-asserted-by":"publisher","first-page":"W331","DOI":"10.1093\/nar\/gkx312","volume":"45","author":"LS Dodda","year":"2017","unstructured":"Dodda LS, De Vaca IC, Tirado-Rives J, Jorgensen WL (2017) LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Res 45(W1):W331\u2013W336","journal-title":"Nucleic Acids Res"},{"key":"737_CR93","doi-asserted-by":"crossref","unstructured":"Ribeiro MT, Singh S, Guestrin C (2016) \u2018Why Should I Trust You?\u2019 Explaining the Predictions of Any Classifier. In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 13\u201317-Augu, pp 1135\u20131144.","DOI":"10.1145\/2939672.2939778"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-023-00737-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-023-00737-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-023-00737-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T01:37:22Z","timestamp":1702863442000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-023-00737-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,28]]},"references-count":93,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["737"],"URL":"https:\/\/doi.org\/10.1186\/s13321-023-00737-5","relation":{},"ISSN":["1758-2946"],"issn-type":[{"type":"electronic","value":"1758-2946"}],"subject":[],"published":{"date-parts":[[2023,7,28]]},"assertion":[{"value":"17 February 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 July 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"69"}}