JIANG, LING, HIRST, JONATHAN D. and DO, HAINAM, 2023. Dynamic Disorder Drives Exciton Dynamics in Diketopyrrolopyrrole-Thiophene-Containing Molecular Crystals JOURNAL OF PHYSICAL CHEMISTRY C. 127(11), 5519-5532
GRIFFITHS, RHYS C., SMITH, FRANCES R., LI, DIYUAN, WYATT, JASMINE, ROGERS, DAVID M., LONG, JED E., CUSIN, LOLA M. L., TIGHE, PATRICK J., LAYFIELD, ROBERT, HIRST, JONATHAN D., MUELLER, MANUEL M. and MITCHELL, NICHOLAS J., 2023. Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation CHEMISTRY-A EUROPEAN JOURNAL.
DAVIES, JOSEPH C., PATTISON, DAVID and HIRST, JONATHAN D., 2023. Machine learning for yield prediction for chemical reactions using in situ sensors JOURNAL OF MOLECULAR GRAPHICS & MODELLING. 118,
LENTZ, JOACHIM C., CAVANAGH, ROBERT, MOLONEY, CARA, PIN, BRUNO FALCONE, KORTSEN, KRISTOFFER, FOWLER, HARRIET R., JACOB, PHILIPPA L., KRUMINS, EDUARDS, CLARK, CHARLOTTE, MACHADO, FABRICIO, BREITKREUZ, NICHOLAS, CALE, BEN, GODDARD, AMY R., HIRST, JONATHAN D., TARESCO, VINCENZO and HOWDLE, STEVEN M., 2022. N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under "greener" reaction conditions POLYMER CHEMISTRY. 13(42), 6032-6045
ROGERS, DAVID M., DO, HAINAM and HIRST, JONATHAN D., 2022. Electronic circular dichroism of proteins computed using a diabatisation scheme MOLECULAR PHYSICS.
SILVA, ARNALDO F., GUEST, ELLEN E., FALCONE, BRUNO N., PICKETT, STEPHEN D., ROGERS, DAVID M. and HIRST, JONATHAN D., 2022. Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4 MOLECULAR PHYSICS.
JIANG, LING, HIRST, JONATHAN D. and DO, HAINAM, 2022. Structure-Property Relationships in Amorphous Thieno[3,2-b]thiophene-Diketopyrrolopyrrole-Thiophene-Containing Polymers JOURNAL OF PHYSICAL CHEMISTRY C. 126(26), 10842-10854
DERBENEV, IVAN N., DOWDEN, JAMES, TWYCROSS, JAMIE and HIRST, JONATHAN D., 2022. Software tools for green and sustainable chemistry CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY. 35,
GUEST, ELLEN E., CERVANTES, LUIS F., PICKETT, STEPHEN D., BROOKS, CHARLES L., III and HIRST, JONATHAN D., 2022. Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4 JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(6), 1458-1470
GAUGHAN, SAMUEL J. H., HIRST, JONATHAN D., CROFT, ANNA K. and JAGER, CHRISTOF M., 2022. Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(3), 591-601
HAYWOOD, ALEXE L., REDSHAW, JOSEPH, HANSON-HEINE, MAGNUS W. D., TAYLOR, ADAM, BROWN, ALEX, MASON, ANDREW M., GAERTNER, THOMAS and HIRST, JONATHAN D., 2022. Kernel Methods for Predicting Yields of Chemical Reactions JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(9), 2077-2092
PACHECO, ANA A. C., DA SILVA FILHO, ARNALDO F., KORTSEN, KRISTOFFER, HANSON-HEINE, MAGNUS W. D., TARESCO, VINCENZO, HIRST, JONATHAN D., LANSALOT, MURIEL, D'AGOSTO, FRANCK and HOWDLE, STEVEN M., 2021. Influence of structure and solubility of chain transfer agents on the RAFT control of dispersion polymerisation in scCO(2) CHEMICAL SCIENCE. 12(3), 1016-1030
ZHOU, JIAJUN, WU, SHIYING, LEE, BOON GIIN, CHEN, TIANWEI, HE, ZIQI, LEI, YUKUN, TANG, BENCAN and HIRST, JONATHAN D., 2021. Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1 MOLECULES. 26(24),
HIRST, JONATHAN D., 2021. Memorial Viewpoint for Nicholas A. Besley JOURNAL OF PHYSICAL CHEMISTRY A. 125(38), 8345-8346
ROBINSON, DAVID, ALARFAJI, SALEH S. and HIRST, JONATHAN D., 2021. Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S-1 -> S-0 Transitions JOURNAL OF PHYSICAL CHEMISTRY A. 125(24), 5237-5245
GUEST, ELLEN E., PICKETT, STEPHEN D. and HIRST, JONATHAN D., 2021. Structural variation of protein-ligand complexes of the first bromodomain of BRD4 ORGANIC & BIOMOLECULAR CHEMISTRY. 19(25), 5632-5641
SEGATTA, FRANCESCO, ROGERS, DAVID M., DYER, NAOMI T., GUEST, ELLEN E., LI, ZHUO, DO, HAINAM, NENOV, ARTUR, GARAVELLI, MARCO and HIRST, JONATHAN D., 2021. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides MOLECULES. 26(2),
JIANG, LING, ROGERS, DAVID M, HIRST, JONATHAN D and DO, HAINAM, 2020. Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene. Journal of chemical theory and computation. 16(8), 5150-5162
AUVRAY, FRANCOIS and HIRST, JONATHAN D., 2020. Unfolding Dynamics of a Photoswitchable Helical Peptide JOURNAL OF PHYSICAL CHEMISTRY B. 124(26), 5380-5392 BAIZ, CARLOS R, BLASIAK, BARTOSZ, BREDENBECK, JENS, CHO, MINHAENG, CHOI, JUN-HO, CORCELLI, STEVEN A, DIJKSTRA, AREND G, FENG, CHI-JUI, GARRETT-ROE, SEAN, GE, NIEN-HUI, HANSON-HEINE, MAGNUS W D, HIRST, JONATHAN D, JANSEN, THOMAS L C, KWAC, KIJEONG, KUBARYCH, KEVIN J, LONDERGAN, CASEY H, MAEKAWA, HIROAKI, REPPERT, MIKE, SAITO, SHINJI, ROY, SANTANU, SKINNER, JAMES L, STOCK, GERHARD, STRAUB, JOHN E, THIELGES, MEGAN C, TOMINAGA, KEISUKE, TOKMAKOFF, ANDREI, TORII, HAJIME, WANG, LU, WEBB, LAUREN J and ZANNI, MARTIN T, 2020. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chemical reviews. 120(15), 7152-7218
HANSON-HEINE, MAGNUS W. D. and HIRST, JONATHAN D., 2020. Mobius and Huckel Cyclacenes with Dewar and Ladenburg Defects JOURNAL OF PHYSICAL CHEMISTRY A. 124(26), 5408-5414 HANSON-HEINE, MAGNUS W. D., ROGERS, DAVID M., WOODWARD, SIMON and HIRST, JONATHAN D., 2020. Dewar Benzenoids Discovered In Carbon Nanobelts JOURNAL OF PHYSICAL CHEMISTRY LETTERS. 11(10), 3769-3772 ROBINSON, HENRY, OATLEY, STEVEN A., ROWEDDER, JAMES E., SLADE, PAWEL, MACDONALD, SIMON J. F., ARGENT, STEPHEN P., HIRST, JONATHAN D., MCINALLY, THOMAS and MOODY, CHRISTOPHER J., 2020. Late-Stage Functionalization by Chan-Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors CHEMISTRY-A EUROPEAN JOURNAL. 26(34), 7678-7684 SOLE-DAURA, ALBERT, RODRIGUEZ-FORTEA, ANTONIO, POBLET, JOSEP M., ROBINSON, DAVID, HIRST, JONATHAN D. and CARBO, JORGE J., 2020. Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases ACS CATALYSIS. 10(22), 13455-13467
YE, SHENG, ZHONG, KAI, ZHANG, JINXIAO, HU, WEI, HIRST, JONATHAN D., ZHANG, GUOZHEN, MUKAMEL, SHAUL and JIANG, JUN, 2020. A Machine Learning Protocol for Predicting Protein Infrared Spectra JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 142(45), 19071-19077
LI, ZHUO and HIRST, JONATHAN D., 2020. Computed optical spectra of SARS-CoV-2 proteins CHEMICAL PHYSICS LETTERS. 758,
SPANKIE, TIMOTHY J., HAYWOOD, ALEXE L., DOTTORINI, TANIA, BARROW, PAUL A. and HIRST, JONATHAN D., 2020. Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid JOURNAL OF MOLECULAR GRAPHICS & MODELLING. 101,
ROGERS, DAVID M., JASIM, SARAH B., DYER, NAOMI T., AUVRAY, FRANCOIS, REFREGIERS, MATTHIEU and HIRST, JONATHAN D., 2019. Electronic Circular Dichroism Spectroscopy of Proteins CHEM. 5(11), 2751-2774 AUVRAY, FRANCOIS, DENNETIERE, DAVID, GIULIANI, ALEXANDRE, JAMME, FREDERIC, WIEN, FRANK, NAY, BASTIEN, ZIRAH, SEVERINE, POLACK, FRANCOIS, MENNEGLIER, CLAUDE, LAGARDE, BRUNO, HIRST, JONATHAN D. and REFREGIERS, MATTHIEU, 2019. Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization STRUCTURAL DYNAMICS-US. 6(5), MICHAELIS, M., HILDEBRAND, N., MEISSNER, R. H., WURZLER, N., LI, Z., HIRST, J. D., MICSONAI, A., KARDOS, J., DELLE PIANE, M. and CIACCHI, L. COLOMBI, 2019. Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra JOURNAL OF PHYSICAL CHEMISTRY B. 123(31), 6694-6704 HILDEBRAND, NILS, MICHAELIS, MONIKA, WURZLER, NINA, LI, ZHUO, HIRST, JONATHAN D., MICSONAI, ANDRAS, KARDOS, JOZSEF, GIL-LEY, ALEJANDRO, BUSSI, GIOVANNI, KOEPPEN, SUSAN, DELLE PIANE, MASSIMO and CIACCHI, LUCIO COLOMBI, 2018. Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica ACS BIOMATERIALS SCIENCE & ENGINEERING. 4(12), 4036-4050 JASIM, SARAH B., LI, ZHUO, GUEST, ELLEN E. and HIRST, JONATHAN D., 2018. DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet JOURNAL OF MOLECULAR BIOLOGY. 430(15), 2196-2202 HUSSEINI FS, ROBINSON D, HUNT NT, PARKER AW and HIRST JD, 2017. Computing infrared spectra of proteins using the exciton model. Journal of computational chemistry. 38(16), 1362-1375 MULHOLLAND, S., TURPIN, E.R., BONEV, B.B. and HIRST, J.D., 2016. Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II Scientific Reports. 6, 21185 HANSON-HEINE, MAGNUS W. D., HUSSEINI, FOUAD S., HIRST, JONATHAN D. and BESLEY, NICHOLAS A., 2016. Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 12(4), 1905-1918 SOLÉ-DAURA A, GOOVAERTS V, STROOBANTS K, ABSILLIS G, JIMÉNEZ-LOZANO P, POBLET JM, HIRST JD, PARAC-VOGT TN and CARBÓ JJ, 2016. Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations. Chemistry A European Journal. 22(43), 15280-15289 LI, ZHUO, ROBINSON, DAVID and HIRST, JONATHAN D., 2015. Vibronic structure in the far-UV electronic circular dichroism spectra of proteins FARADAY DISCUSSIONS. 177, 329-344 AGUADO-ULLATE, SONIA, BAKER, JOHN A., GONZALEZ-GONZALEZ, VANESSA, MUELLER, CHRISTIAN, HIRST, JONATHAN D. and CARBO, JORGE J., 2014. A theoretical study of the activity in Rh-catalysed hydroformylation: the origin of the enhanced activity of the pi-acceptor phosphinine ligand CATALYSIS SCIENCE & TECHNOLOGY. 4(4), 979-987 HIRST, JONATHAN D., GLOWACKI, DAVID R. and BAADEN, MARC, 2014. Molecular simulations and visualization: introduction and overview FARADAY DISCUSSIONS. 169, 9-22 ELEANOR R TURPIN, HUEY-JEN FANG, NEIL R. THOMAS and JONATHAN D. HIRST, 2013. Cooperativity and Site Selectivity in the Ileal Lipid Binding Protein Biochemistry. 52(27), 4723–4733 HILL RE, HUNT NT and HIRST JD, 2013. Studying biomacromolecules with two-dimensional infrared spectroscopy. Advances in protein chemistry and structural biology. 93, 1-36 GAIGEOT, MARIE-PIERRE, BESLEY, NICHOLAS A and HIRST, JONATHAN D, 2011. Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide. Journal of Physical Chemistry. B. 115(18), 5526-35 OAKLEY, MARK T, DO, HAINAM, HIRST, JONATHAN D and WHEATLEY, RICHARD J, 2011. First principles predictions of thermophysical properties of refrigerant mixtures. Journal of Chemical Physics. 134(11), 114518 ROBINSON, D., BESLEY, N.A., O'SHEA, P. and HIRST, J.D., 2011. Water order profiles on phospholipid/cholesterol membrane bilayer surfaces Journal of Computational Chemistry. 32(12), 2613-2618 ROBINSON, D., BESLEY, N.A., O'SHEA, P. and HIRST, J.D., 2011. Di-8-ANEPPS emission spectra in phospholipid/cholesterol membranes: a theoretical study Journal of Physical Chemistry B. 115(14), 4160-4167 DO, H., HIRST, J.D. and WHEATLEY, R.J., 2011. Rapid calculation of partition functions and free energies of fluids Journal of Chemical Physics. 135(17), 174105 DO, H, WHEATLEY, RJ and HIRST, JD, 2011. Molecular Simulation Of The Binary Mixture Of 1-1-1-2-Tetrafluoroethane And Carbon Dioxide Physical Chemistry Chemical Physics. 13(34), 15708-15713 BAKER, JA and HIRST, JD, 2011. Molecular Dynamics Simulations Using Graphics Processing Units Molecular Informatics. 30(6-7), 498-504 DO, HAINAM, WHEATLEY, RICHARD J and HIRST, JONATHAN D, 2010. Gibbs ensemble Monte Carlo simulations of binary mixtures of methane, difluoromethane, and carbon dioxide. Journal of Physical Chemistry. B. 114(11), 3879-86 JIANG, JUN, ABRAMAVICIUS, DARIUS, BULHELLER, BENJAMIN M, HIRST, JONATHAN D and MUKAMEL, SHAUL, 2010. Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: combined QM and MM simulations. Journal of Physical Chemistry B. 114(24), 8270-8277 HUSSAIN, ABRAR, MELVILLE, JAMES L and HIRST, JONATHAN D, 2010. Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin. Journal of Computer-Aided Molecular Design. 24(1), 1-15 BROMLEY, ELIZABETH H C, CHANNON, KEVIN J, KING, PATRICK J S, MAHMOUD, ZAHRA N, BANWELL, ELEANOR F, BUTLER, MICHAEL F, CRUMP, MATTHEW P, DAFFORN, TIMOTHY R, HICKS, MATTHEW R, HIRST, JONATHAN D and RODGER,, 2010. Assembly pathway of a designed alpha-helical protein fiber. Biophysical Journal. 98(8), 1668-76 ABRAMAVICIUS, D., JIANG, J., BULHELLER, B.M., HIRST, J.D. and MUKAMEL, S., 2010. Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backbone Journal of the American Chemical Society. 132(22), 7769-7775 ROBINSON, D., BESLEY, N. A., LUNT, E. A. M., O'SHEA, P. and HIRST, J. D., 2009. Electronic structure of 5-hydroxyindole: from gas phase to explicit solvation. Journal of Physical Chemistry B. 113(8), 2535-2541 SPOWAGE, BENSON M, BRUCE, CRAIG L and HIRST, JONATHAN D, 2009. Interpretable correlation descriptors for quantitative structure-activity relationships. Journal of Cheminformatics. 1, 22 BACARDIT, J., STOUT, M., HIRST, J.D., VALENCIA, A., SMITH, R.E. and KRASNOGOR, N., 2009. Automated alphabet reduction for protein datasets BMC Bioinformatics. 10, 6 BULHELLER, B.M. and HIRST, J.D., 2009. Dichrocalc - circular and linear dichroism online Bioinformatics. 25, 539-540 STOUT, M., BACARDIT, J., HIRST, J.D., SMITH, R.E. and KRASNOGOR, N., 2009. Prediction of Topological Contacts in Proteins Using Learning Classifier Systems Soft Computing. 13, 245-258 MELVILLE, J.L., BURKE, E.K. and HIRST, J.D., 2009. Machine learning in virtual screening Combinatorial Chemistry & High Throughput Screening. 12, 332-343 ROBINSON, D., BESLEY, N.A., O'SHEA, P. and HIRST, J.D., 2009. Calculating the fluorescence of 5-hydroxytryptophan in proteins Journal of Physical Chemistry B. 113(43), 14521-14528 BULHELLER, B.M., RODGER, A., HICKS, M.R., DAFFORN, T.R., SERPELL, L.C., MARSHALL, K.E., BROMLEY, E.H.C., KING, P.J.S., CHANNON, K.J., WOOLFSON, D.N. and HIRST, JD, 2009. Flow linear dichroism of some prototypical proteins Journal of the American Chemical Society. 131(37), 13305-13314 BULHELLER, B.M., PANTOŞ , G.D., SANDERS, J.K.M. and HIRST, J.D., 2009. Electronic structure and circular dichroism spectroscopy of naphthalenediimide nanotubes Physical Chemistry Chemical Physics. 11(29), 6060-6065 EVANS, C. L., LONG, J. E., GALLAGHER, T. R., HIRST, J. D. and SEARLE, M. S., 2008. Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation PROTEINS -NEW YORK-. VOL 71(NUMBER 1), 227-240
STOUT, M., BACARDIT, J., HIRST, J.D. and KRASNOGOR, N., 2008. Prediction of recursive convex hull class assignments for protein residues Bioinformatics. 24(7), 916-923 MARK T. OAKLEY, DANIEL BARTHEL, YURI BYKOV, JON M. GARIBALDI, EDMUND K. BURKE, NATALIO KRASNOGOR, JONATHAN D. HIRST, 2008. Search Strategies in Structural Bioinformatics Current Protein and Peptide Science. 9, 260-274 HAMBY, S.E. and HIRST, J.D., 2008. Prediction of glycosylation sites using random forests. BMC bioinformatics. 9(1), 500
BULHELLER, B.M., MILES, A.J., WALLACE, B.A. and HIRST, J.D., 2008. Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra Journal of Physical Chemistry B. 112(6), 1866-1874 VINCENT, E, SAXTON, J, BAKER-GLENN, C, MOAL, I, HIRST, J D, PATTENDEN, G and SHAW, P E, 2007. Effects of ulapualide A and synthetic macrolide analogues on actin dynamics and gene regulation. Cellular and Molecular Life Sciences. 64(4), 487-97 DANIEL BARTHEL, JONATHAN D. HIRST, JACEK BLAZEWICZ, EDMUND K. BURKE, NATALIO KRASNOGOR, 2007. ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information. BMC Bioinformatics. 8, 416 MELVILLE, JAMES L, RILEY, JENNA F and HIRST, JONATHAN D, 2007. Similarity by compression. Journal of chemical information and modeling. 47(1), 25-33 BRUCE, C.L., MELVILLE, J.L., PICKETT, S.D. and HIRST, J.D., 2007. Contemporary QSAR Classifiers Compared Journal of Chemical Information & Modeling. 47(1), 219-227 MELVILLE, JAMES L and HIRST, JONATHAN D, 2007. TMACC: Interpretable Correlation Descriptors for Quantitative Structure-Activity Relationships. Journal of chemical information and modeling. 47(2), 626-34 MELVILLE, JAMES L, MOAL, IAIN H, BAKER-GLENN, CHARLES, SHAW, PETER E, PATTENDEN, GERALD and HIRST, JONATHAN D, 2007. The structural determinants of macrolide-actin binding: in silico insights. Biophysical Journal. 92(11), 3862-7 BULHELLER, BENJAMIN M, RODGER, ALISON and HIRST, JONATHAN D, 2007. Circular and linear dichroism of proteins. Physical Chemistry Chemical Physics. 9(17), 2020-35 OAKLEY, M.T., GUICHARD, G. and HIRST, J.D., 2007. Calculations on the Electronic Excited States of Ureas and Oligoureas Journal of Physical Chemistry B. 111(12), 3274-3279 OAKLEY, M.T. and HIRST, J.D., 2006. Charge-transfer transitions in protein circular dichroism calculations Journal of the American Chemical Society. 128(38), 12414-12415 STOUT,M., BACARDIT,J., HIRST,J.D., KRASNOGOR,N. and BLAZEWICZ,J., 2006. From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems. In: Applications of Evolutionary Computing.EvoWorkshops 2006: EvoBIO, EvoCOMNET, EvoHOT EvoIASP, EvoINTERACTION, EvoMUSART, and EvoSTOC Budapest, Hungary, April 10-12, 2006 Proceedings Springer; Berlin. 208-220 BACARDIT, J., STOUT, M., KRASNOGOR, N., HIRST, J. D. and BLAZEWICZ, J., 2006. Coordination Number Prediction Using Learning Classifier Systems: Performance and interpretability GECCO -CONFERENCE-. CONF 8(VOL 1), 247-254
STOUT, M., BACARDIT, J., BLAZEWICZ, J., HIRST, J.D. and KRASNOGOR, N., 2006. Prediction of Residue Exposure and Contact Number for Simplified HP Lattice Model Proteins using Learning Classifier Systems In: 7th International FLINS Conference. 601-608
OAKLEY, M. T., BULHELLER, B. M. and HIRST, J. D., 2006. First-principles calculations of protein circular dichroism in the far-ultraviolet and beyond Chirality. VOL 18(NUMBER 5), 340-347 LA COUR JANSEN, T., DIJKSTRA, A. G., WATSON, T. M., HIRST, J. D. and KNOESTER, J., 2006. Modeling the amide I bands of small peptides (9 pages) Journal of Chemical Physics. VOL 125(NUMB 4), 044312 ROGERS, D. M., HIRST, J. D., LEE, E. P. and WRIGHT, T. G., 2006. Ab initio study of the toluene dimer Chemical Physics Letters. VOL 427(NUMBER 4-6), 410-413 MELVILLE, J.L., LOVELOCK, K.R.J., WILSON, C., ALLBUTT, B., BURKE, E.K., LYGO, B. and HIRST, J.D., 2005. Exploring phase-transfer catalysis with molecular dynamics and 3D/4D quantitative structure-selectivity relationships Journal of Chemical Information and Modeling. 45(4), 971-981 OAKLEY, M.T., GARIBALDI, J.M. and HIRST, J.D., 2005. Lattice models of peptide aggregation: evaluation of conformational search algorithms Journal of Computational Chemistry. 26(15), 1638-1646 WOOD, M.J. and HIRST, J.D., 2005. Protein secondary structure prediction with dihedral angles Proteins. 59(3), 476-481 BLACKBURNE, B. P. and HIRST, J. D., 2005. Population dynamics simulations of functional model proteins (9 pages) Journal of Chemical Physics. VOL 123(NUMB 15), 154907 WATSON, T. M. and HIRST, J. D., 2005. Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin Molecular Physics. VOL 103(NUMB 11/12), 1531-1546 MCNEANY, T.J. and HIRST, J.D., 2005. Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Non-Parametric Regression. Journal of Chemical Information and Computer Sciences. 45, 768-776 MELVILLE, J.L., ANDREWS, B.I., LYGO, B. and HIRST, J.D., 2004. Computational screening of combinatorial catalyst libraries Chemical Communications. 12, 1410-1411 LYGO, B., ANDREWS, B. I., HIRST, J. D., MELVILLE, J. L., PETERSON, J. A. and SLACK, D., 2004. Rapid screening of cinchona alkaloid derived phase-transfer catalysts. Application in the optimization of a glycine imine alkylation Chimica Oggi. VOL 22(PART 9), 8-11
WATSON, T.M. and HIRST, J.D., 2004. Calculating vibrational frequencies of amides: From formamide to concanavalin A Physical Chemistry Chemical Physics. 6(5), 998-1005 BESLEY, N.A., OAKLEY, M.T., COWAN, A.J. and HIRST, J.D., 2004. A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides Journal of the American Chemical Society. 126(41), 13502-13511 MELVILLE, J. L. and HIRST, J. D., 2004. On the Stability of CoMFA Models Journal of Chemical Information and Computer Sciences. VOL 44(PART 4), 1294-1300 GILBERT, A. T. and HIRST, J. D., 2004. Charge-transfer transitions in protein circular dichroism spectra Journal of Molecular Structure. VOL 675(NUMBER 1-3), 53-60
ROGERS, D. M. and HIRST, J. D., 2004. Calculations of Protein Circular Dichroism From First Principles Chirality. VOL 16(PART 4), 234-243 WATSON, T. M. and HIRST, J. D., 2004. Vibrational analysis of capped [Leu]enkephalin Physical Chemistry Chemical Physics. 6(10), 2580-2587 ROGERS, D. M. and HIRST, J. D., 2003. Ab Initio Study of Aromatic Side Chains of Amino Acids in Gas Phase and Solution Journal of Physical Chemistry A. VOL 107(PART 50), 11191-11200 HIRST, J. D., BHATTACHARJEE, S. and ONUFRIEV, A. V., 2003. Theoretical studies of time-resolved spectroscopy of protein folding Faraday Discussions. ISSU 122, 253-268 BHATTACHARJEE, S., TOTH, G., LOVAS, S. and HIRST, J. D., 2003. Influence of Tyrosine on the Electronic Circular Dichroism of Helical Peptides JOURNAL OF PHYSICAL CHEMISTRY B. 107(33), 8682-8688 HIRST, J. D., COLELLA, K. and GILBERT, A. T. B., 2003. Electronic Circular Dichroism of Proteins from First-Principles Calculations JOURNAL OF PHYSICAL CHEMISTRY B. VOL 107(PART 42), 11813-11819 COX, K., WATSON, T., SOULTANAS, P. and HIRST, J. D., 2003. Molecular Dynamics Simulations of a Helicase Proteins. VOL 52(PART 2), 254-262 BLACKBURNE, B. P. and HIRST, J. D., 2003. Three-dimensional functional model proteins: Structure function and evolution Journal of Chemical Physics. VOL 119(PART 6), 3453-3460 WATSON, T. M. and HIRST, J. D., 2003. Influence of Electrostatic Environment on the Vibrational Frequencies of Proteins Journal of Physical Chemistry A. VOL 107(PART 35), 6843-6849 WATSON, T. M. and HIRST, J. D., 2002. Density Functional Theory Vibrational Frequencies of Amides and Amide Dimers Journal of Physical Chemistry A. VOL 106(PART 34), 7858-7867 ANDREW, C. D., BHATTACHARJEE, S., KOKKONI, N., HIRST, J. D., JONES, G. R. and DOIG, A. J., 2002. Stabilizing Interactions between Aromatic and Basic Side Chains in alpha-Helical Peptides and Proteins. Tyrosine Effects on Helix Circular Dichroism Journal of the American Chemical Society. VOL 124(PART 43), 12706-12714 RODGER, A., RAJENDRA, J., MARRINGTON, R., ARDHAMMAR, M., NORDEN, B., HIRST, J. D., GILBERT, A. T. B., DAFFORN, T. R., HALSALL, D. J. and WOOLHEAD, C. A., 2002. Flow oriented linear dichroism to probe protein orientation in membrane environments Physical Chemistry Chemical Physics. VOL 4(NUMB 16), 4051-4057 HIRST, J. D., MCNEANY, T. J., HOWE, T. and WHITEHEAD, L., 2002. Application of Non-Parametric Regression to Quantitative Structure-Activity Relationships Bioorganic and Medicinal Chemistry. VOL 10(NUMBER 4), 1037-1041 DANG, Z. and HIRST, J. D., 2001. Short Hydrogen Bonds, Circular Dichroism, and Over-Estimates of Peptide Helicity Angewandte Chemie International Edition. VOL 40(PART 19), 3619-3621
HIRST, J., 2001. Evolutionary Landscape of Functional Model Proteins Abstracts of Papers of the American Chemical Society. 221, 102-COMP
BLACKBURNE, B. P. and HIRST, J. D., 2001. Evolution of functional model proteins Journal of Chemical Physics. VOL 115(PART 4), 1935-1942 HIRST, J.D., 2001. Computer Modeling of Protein Structure. In: Modern Protein Chemistry Practical Aspects 123-143
HIRST, J., 2001. Calculating Electronic Structure and Optical Properties of Proteins Abstracts of Papers of the American Chemical Society. 221, 320-PHYS
TOTH, G., KOVER, K.E., HIRST, J.D., MURPHY, R.F. and LOVAS, S., 2001. Alpha-helix Stabilising Aromatic-Backbone Interactions. In: Peptides, The Wave of the Future: Proceedings of the Second International and Seventeenth American Peptide Symposium 303-305
HIRST, J., 2001. Application of Non-parametric Regression to QSAR Abstracts of Papers of the American Chemical Society. 221, 243-COMP
BESLEY, N. A., BRIENNE, M.-J. and HIRST, J. D., 2000. Electronic Structure of a Rigid Cyclic Diamide Journal of Physical Chemistry B. VOL 104(PART 51), 12371-12377 BESLEY, N. A. and HIRST, J. D., 2000. Hydrogen bonding in protein circular dichroism calculations Journal of Molecular Structure. VOL 506(NUMBER 1-3), 161-167
CONSTANS, P. and HIRST, J., 2000. Nonparametric Regression Applied to Quantitative Stucture - Activity Relationships Journal of Chemical Information and Computer Sciences. 40, 452-459 BESLEY, N. A. and HIRST, J. D., 1999. Ab Initio Study of the Electronic Spectrum of Formamide with Explicit Solvent Journal of the American Chemical Society. VOL 121(NUMBER 37), 8559-8566 HIRST, J.D. and BESLEY, N.A., 1999. Theoretical Studies Towards Quantitative Protein Circular Dichroism Calculations Journal of the American Chemical Society. 121, 9636-9644 BESLEY, N. A. and HIRST, J. D., 1998. Ab Initio Study of the Effect of Solvation on the Electronic Spectra of Formamide and N-Methylacetamide JOURNAL OF PHYSICAL CHEMISTRY A. VOL 102(NUMBER 52), 10791-10797
HIRST, J. D. and PERSSON, B. J., 1998. Ab Initio Calculations of the Vibrational and Electronic Spectra of Diketopiperazine JOURNAL OF PHYSICAL CHEMISTRY A. VOL 102(NUMBER 38), 7519-7524
VIETH, M., HIRST, J. D., KOLINSKI, A. and BROOKS, C. L., 1998. Assessing Energy Functions for Flexible Docking Journal of Computational Chemistry. VOL 19(NUMBER 14), 1612-1622 VIETH, M., HIRST, J. D. and BROOKS, C. L., 1998. Do active site conformations of small ligands correspond to low free-energy solution structures? Journal of Computer-Aided Molecular Design. 12(6), 563-572 HIRST, J.D., 1998. Predicting Ligand Binding Energies Current Opinion in Drug Discovery & Development. 1, 28-33
VIETH, M., HIRST, J. D., DOMINY, B. N., DAIGLER, H. and BROOKS, C. L., 1998. Assessing Search Strategies for Flexible Docking Journal of Computational Chemistry. VOL 19(NUMBER 14), 1623-1631 HIRST, J. D., HIRST, D. M. and BROOKS, C. L., 1996. Ab Initio Calculations of the Excited States of Formamide Journal of Physical Chemistry. VOL 100(NUMBER 32), 13487-13491 HIRST, J. D., VIETH, M., SKOLNICK, J. and BROOKS, C. L., 1996. Predicting leucine zipper structures from sequence Protein Engineering. VOL 9(NUMBER 8), 657-662 KING, R.D., HIRST, J.D. and STERNBERG, M.J., 1995. Comparison of Artificial-Intelligence Methods for Modeling Pharmaceutical Qsars Applied Artificial Intelligence. 9(2), 213-233 HIRST, J. D. and BROOKS, C. L., 1995. Molecular Dynamics Simulations of Isolated Helices of Myoglobin Biochemistry. VOL 34(NUMBER 23), 7614 HIRST, J. D. and BROOKS, C. L., 1994. Helicity, Circular Dichroism and Molecular Dynamics of Proteins Journal of Molecular Biology. VOL 243(NUMBER 2), 173 KING, R.D., HIRST, J.D. and STERNBERG, M.J., 1993. New Approaches to QSAR: Neural Networks and Machine Learning 1, 279-290
HIRST, J.D. and STERNBERG, M.J., 1991. Prediction of ATP-Binding Motifs: A Comparison of a Perceptron-Type Neural Network and a Consensus Sequence Method Protein Engineering. 4, 615-623
SMITH, R.E, LIANG, M, BACARDIT, J, STOUT, M and KRASNOGOR, N. & HIRST, J.D., A Learning Classifier System with Mutual-Information-Based Fitness Evolutionary Intelligence. 3, 31-50 TURPIN, ELEANOR R., FANG, HUEY-JEN, THOMAS, NEIL R. and HIRST, JONATHAN D., Cooperativity and Site Selectivity in the Ileal Lipid Binding Protein BIOCHEMISTRY. 52(27), 4723-4733