cached image

David L. Beveridge, PhD - Publications

Affiliations: 
Wesleyan University, Middletown, CT, United States 
Area:
Theoretical and computational chemistry
Website:
http://www.wesleyan.edu/molbiophys/Faculty/Beveridge/beveridge.cv.htm

165/173 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Lakhani B, Thayer KM, Black E, Beveridge DL. Spectral analysis of molecular dynamics simulations on PDZ: MD sectors. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 31262238 DOI: 10.1080/07391102.2019.1588169  0.48
2018 Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Toward a Universal Structural and Energetic Model for Prokaryotic Promoters. Biophysical Journal. PMID 30172386 DOI: 10.1016/j.bpj.2018.08.002  0.48
2017 Thayer KM, Lakhani B, Beveridge DL. A Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit. The Journal of Physical Chemistry. B. PMID 28489401 DOI: 10.1021/acs.jpcb.7b02083  0.48
2017 Lakhani B, Thayer KM, Hingorani MM, Beveridge DL. Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein. The Journal of Physical Chemistry. B. PMID 28135092 DOI: 10.1021/acs.jpcb.6b11976  0.48
2015 Lakhani B, Black E, Beveridge DL. 56 Molecular dynamics simulation studies of protein sectors: motional correlations. Journal of Biomolecular Structure & Dynamics. 33: 38. PMID 26103267 DOI: 10.1080/07391102.2015.1032672  0.48
2014 Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevi?i?t? D, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. 42: 12272-83. PMID 25260586 DOI: 10.1093/nar/gku855  0.84
2014 Khandelwal G, Lee RA, Jayaram B, Beveridge DL. A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes. Biophysical Journal. 106: 2465-73. PMID 24896126 DOI: 10.1016/j.bpj.2014.04.029  0.84
2012 Dixit SB, Mezei M, Beveridge DL. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. Journal of Biosciences. 37: 399-421. PMID 22750979 DOI: 10.1007/s12038-012-9223-5  0.84
2012 Beveridge DL, Cheatham TE, Mezei M. The ABCs of molecular dynamics simulations on B-DNA, circa 2012. Journal of Biosciences. 37: 379-97. PMID 22750978 DOI: 10.1007/s12038-012-9222-6  0.84
2012 Wheatley EG, Pieniazek SN, Mukerji I, Beveridge DL. Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)â‚„. Biophysical Journal. 102: 552-60. PMID 22325278 DOI: 10.1016/j.bpj.2011.11.4023  0.84
2012 Wheatley EG, Pieniazek SN, Vitoc I, Mukerji I, Beveridge DL. Chapter 5: Molecular dynamics structure prediction of a novel protein-DNA complex: Two HU proteins with a DNA four-way junction Rsc Biomolecular Sciences. 111-128.  0.84
2011 Pieniazek SN, Hingorani MM, Beveridge DL. Dynamical allosterism in the mechanism of action of DNA mismatch repair protein MutS. Biophysical Journal. 101: 1730-9. PMID 21961599 DOI: 10.1016/j.bpj.2011.08.039  0.84
2011 Kormos BL, Pieniazek SN, Beveridge DL, Baranger AM. U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. Biopolymers. 95: 591-606. PMID 21384338 DOI: 10.1002/bip.21616  0.84
2010 Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research. 38: 299-313. PMID 19850719 DOI: 10.1093/nar/gkp834  0.84
2009 Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society. 131: 1724-35. PMID 19191698 DOI: 10.1021/ja805405a  0.84
2008 Singhal P, Jayaram B, Dixit SB, Beveridge DL. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophysical Journal. 94: 4173-83. PMID 18326660 DOI: 10.1529/biophysj.107.116392  0.84
2008 Knee KM, Dixit SB, Aitken CE, Ponomarev S, Beveridge DL, Mukerji I. Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophysical Journal. 95: 257-72. PMID 18326653 DOI: 10.1529/biophysj.107.117606  0.84
2008 Anunciado D, Agumeh M, Kormos BL, Beveridge DL, Knee JL, Baranger AM. Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements. The Journal of Physical Chemistry. B. 112: 6122-30. PMID 18293956 DOI: 10.1021/jp076896c  0.84
2007 Yan Z, Sikri S, Beveridge DL, Baranger AM. Identification of an aminoacridine derivative that binds to RNA tetraloops. Journal of Medicinal Chemistry. 50: 4096-104. PMID 17665894 DOI: 10.1021/jm070305p  0.84
2007 Zhong W, Dixit SB, Mallis RJ, Arthanari H, Lugovskoy AA, Beveridge DL, Wagner G, Reinherz EL. CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications. Journal of Molecular Biology. 372: 535-48. PMID 17658550 DOI: 10.1016/j.jmb.2007.06.057  0.84
2007 Kormos BL, Benitex Y, Baranger AM, Beveridge DL. Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model. Journal of Molecular Biology. 371: 1405-19. PMID 17603075 DOI: 10.1016/j.jmb.2007.06.003  0.84
2007 Kormos BL, Baranger AM, Beveridge DL. A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. Journal of Structural Biology. 157: 500-13. PMID 17194603 DOI: 10.1016/j.jsb.2006.10.022  0.84
2006 Kormos BL, Baranger AM, Beveridge DL. Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex. Journal of the American Chemical Society. 128: 8992-3. PMID 16834346 DOI: 10.1021/ja0606071  0.84
2006 Dixit SB, Ponomarev SY, Beveridge DL. Root mean square deviation probability analysis of molecular dynamics trajectories on DNA. Journal of Chemical Information and Modeling. 46: 1084-93. PMID 16711728 DOI: 10.1021/ci0504925  0.84
2006 Dixit SB, Beveridge DL. Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. Bioinformatics (Oxford, England). 22: 1007-9. PMID 16489208 DOI: 10.1093/bioinformatics/btl059  0.84
2006 Zhao Y, Kormos BL, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface. Biopolymers. 81: 256-69. PMID 16278830 DOI: 10.1002/bip.20408  0.84
2006 Beveridge DL, Dixit SB, Kormos BL, Baranger AM, Jayaram B. Molecular dynamics simulations and free energy calculations on protein-nucleic acid complexes Computational Studies of Rna and Dna. 211-234. DOI: 10.1007/978-1-4020-4851-3_8  0.84
2005 Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophysical Journal. 89: 3721-40. PMID 16169978 DOI: 10.1529/biophysj.105.067397  0.84
2005 Dixit SB, Andrews DQ, Beveridge DL. Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences. Biophysical Journal. 88: 3147-57. PMID 15731390 DOI: 10.1529/biophysj.104.053843  0.84
2005 Dixit SB, Beveridge DL. Axis curvature and ligand induced bending in the CAP-DNA oligomers. Biophysical Journal. 88: L04-6. PMID 15556974 DOI: 10.1529/biophysj.104.053058  0.84
2004 Dixit SB, Pitici F, Beveridge DL. Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy. Biopolymers. 75: 468-79. PMID 15526331 DOI: 10.1002/bip.20157  0.84
2004 Ponomarev SY, Thayer KM, Beveridge DL. Ion motions in molecular dynamics simulations on DNA. Proceedings of the National Academy of Sciences of the United States of America. 101: 14771-5. PMID 15465909 DOI: 10.1073/pnas.0406435101  0.84
2004 Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, et al. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophysical Journal. 87: 3799-813. PMID 15326025 DOI: 10.1529/biophysj.104.045252  0.84
2004 Beveridge DL, Dixit SB, Barreiro G, Thayer KM. Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. Biopolymers. 73: 380-403. PMID 14755574 DOI: 10.1002/bip.20019  0.84
2004 Byun KS, Beveridge DL. Molecular dynamics simulations of papilloma virus E2 DNA sequences: dynamical models for oligonucleotide structures in solution. Biopolymers. 73: 369-79. PMID 14755573 DOI: 10.1002/bip.10527  0.84
2004 Beveridge DL. Biopolymers: Preface Biopolymers. 73: 326. DOI: 10.1002/bip.20026  0.84
2003 Arthanari H, McConnell KJ, Beger R, Young MA, Beveridge DL, Bolton PH. Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers. 68: 3-15. PMID 12579576 DOI: 10.1002/bip.10263  0.84
2002 Pitici F, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity? Biopolymers. 65: 424-35. PMID 12434430 DOI: 10.1002/bip.10251  0.84
2002 Thayer KM, Beveridge DL. Hidden Markov models from molecular dynamics simulations on DNA. Proceedings of the National Academy of Sciences of the United States of America. 99: 8642-7. PMID 12072566 DOI: 10.1073/pnas.132148699  0.84
2002 Jayaram B, McConnell K, Dixit SB, Das A, Beveridge DL. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. Journal of Computational Chemistry. 23: 1-14. PMID 11913374 DOI: 10.1002/jcc.10009  0.84
2002 Liu Y, Beveridge DL. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. Proteins. 46: 128-46. PMID 11746709 DOI: 10.1002/prot.10020  0.84
2002 Kombo DC, Jayaram B, Mcconnell KJ, Beveridge DL. Calculation of the affinity of the λ repressor-operator complex based on free energy component analysis Molecular Simulation. 28: 187-211. DOI: 10.1080/08927020211970  0.84
2001 McConnell KJ, Beveridge DL. Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility. Journal of Molecular Biology. 314: 23-40. PMID 11724529 DOI: 10.1006/jmbi.2001.4926  0.84
2001 Kombo DC, McConnell KJ, Young MA, Beveridge DL. Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator. Biopolymers. 59: 205-25. PMID 11473347 DOI: 10.1002/1097-0282(20011005)59:4<205::AID-BIP1019>3.0.CO;2-4  0.84
2001 Blakaj DM, McConnell KJ, Beveridge DL, Baranger AM. Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex. Journal of the American Chemical Society. 123: 2548-51. PMID 11456923 DOI: 10.1021/ja005538j  0.84
2001 Liu Y, Beveridge DL. A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data. Journal of Biomolecular Structure & Dynamics. 18: 505-26. PMID 11245247 DOI: 10.1080/07391102.2001.10506684  0.84
2000 McConnell KJ, Beveridge DL. DNA structure: what's in charge? Journal of Molecular Biology. 304: 803-20. PMID 11124028 DOI: 10.1006/jmbi.2000.4167  0.84
2000 Kombo DC, Young MA, Beveridge DL. One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein. Biopolymers. 53: 596-605. PMID 10766954 DOI: 10.1002/(SICI)1097-0282(200006)53:7<596::AID-BIP6>3.0.CO;2-U  0.84
2000 Beveridge DL, McConnell KJ. Nucleic acids: theory and computer simulation, Y2K. Current Opinion in Structural Biology. 10: 182-96. PMID 10753816 DOI: 10.1016/S0959-440X(00)00076-2  0.84
2000 Kombo DC, Young MA, Beveridge DL. Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions. Proteins. 39: 212-5. PMID 10737942 DOI: 10.1002/(SICI)1097-0134(20000515)39:3<212::AID-PROT30>3.0.CO;2-C  0.84
1999 Sprous D, Young MA, Beveridge DL. Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature. Journal of Molecular Biology. 285: 1623-32. PMID 9917401 DOI: 10.1006/jmbi.1998.2241  0.84
1999 Jayaram B, McConnell KJ, Dixit SB, Beveridge DL. Free Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease-DNA Complex Journal of Computational Physics. 151: 333-357. DOI: 10.1006/jcph.1998.6173  0.84
1999 Kombo DC, Ravishanker G, Rackovsky S, Beveridge DL. Computational Analysis of Variants of the Operator Binding Domain of the Bacteriophage λ Repressor International Journal of Quantum Chemistry. 75: 313-325.  0.84
1998 Young MA, Beveridge DL. Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. Journal of Molecular Biology. 281: 675-87. PMID 9710539 DOI: 10.1006/jmbi.1998.1962  0.84
1998 Jayaram B, Liu Y, Beveridge DL. A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts Journal of Chemical Physics. 109: 1465-1471. DOI: 10.1063/1.476697  0.84
1998 Jayaram B, Sprous D, Young MA, Beveridge DL. Free energy analysis of the conformational preferences of A and B forms of DNA in solution Journal of the American Chemical Society. 120: 10629-10633. DOI: 10.1021/ja981307p  0.84
1998 Beveridge DL, Young MA, Sprous D. Modeling of DNA via Molecular Dynamics Simulation: Structure, Bending, and Conformational Tansitions Acs Symposium Series. 682: 260-284.  0.84
1998 Jayaram B, Sprous D, Beveridge DL. Solvation free energy of biomacromolecules: Parameters for a modified generalized born model consistent with the AMBER force field Journal of Physical Chemistry B. 102: 9571-9576.  0.84
1998 Young MA, Jayaram B, Beveridge DL. Local dielectric environment of B-DNA in solution: Results from a 14 ns molecular dynamics trajectory Journal of Physical Chemistry B. 102: 7666-7669.  0.84
1998 Sprous D, Young MA, Beveridge DL. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: Theoretical considerations of the a ⇔ B transition Journal of Physical Chemistry B. 102: 4658-4667.  0.84
1997 Young MA, Ravishanker G, Beveridge DL. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. Biophysical Journal. 73: 2313-36. PMID 9370428 DOI: 10.1016/S0006-3495(97)78263-8  0.84
1997 Flatters D, Young M, Beveridge DL, Lavery R. Conformational properties of the TATA-box binding sequence of DNA. Journal of Biomolecular Structure & Dynamics. 14: 757-65. PMID 9195344 DOI: 10.1080/07391102.1997.10508178  0.84
1997 Young MA, Jayaram B, Beveridge DL. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets Journal of the American Chemical Society. 119: 59-69. DOI: 10.1021/ja960459m  0.84
1997 Ravishanker G, Auffinger P, Langley DR, Jayaram B, Young MA, Beveridge DL. Treatment of Counterions in Computer Simulations of DNA Reviews in Computational Chemistry. 11: 317-372.  0.84
1996 Jayaram B, Beveridge DL. Modeling DNA in aqueous solutions: Theoretical and computer simulation studies on the ion atmosphere of DNA Annual Review of Biophysics and Biomolecular Structure. 25: 367-394. PMID 8800475  0.84
1995 Young MA, Srinivasan J, Goljer I, Kumar S, Beveridge DL, Bolton PH. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods in Enzymology. 261: 121-44. PMID 8569492 DOI: 10.1016/S0076-6879(95)61007-3  0.84
1995 Young MA, Ravishanker G, Beveridge DL, Berman HM. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophysical Journal. 68: 2454-68. PMID 7647248 DOI: 10.1016/S0006-3495(95)80427-3  0.84
1995 Auffinger P, Beveridge DL. A simple test for evaluating the truncation effects in simulations of systems involving charged groups Chemical Physics Letters. 234: 413-415. DOI: 10.1016/0009-2614(95)00065-C  0.84
1995 Beveridge DL, McConnell KJ, Young MA, Vijayakumar S, Ravishanker G. Molecular dynamics simulations of DNA and a protein-DNA complex including solvent Molecular Engineering. 5: 255-269. DOI: 10.1007/BF00999594  0.84
1995 Vijayakumar S, Ravishanker G, Pratt RF, Beveridge DL. Molecular dynamics simulation of a class A β-lactamase: Structural and mechanistic implications Journal of the American Chemical Society. 117: 1722-1730.  0.84
1994 Ptaszek LM, Vijayakumar S, Ravishanker G, Beveridge DL. Molecular dynamics studies of the human CD4 protein. Biopolymers. 34: 1145-53. PMID 7948728 DOI: 10.1002/bip.360340904  0.84
1994 Harte WE, Beveridge DL. Probing structure-function relationships in human immunodeficiency virus type 1 protease via molecular dynamics simulation. Methods in Enzymology. 241: 178-95. PMID 7854178  0.84
1994 Balasubramanian S, Nirmala R, Beveridge DL, Bolton PH. Comparison of the 13C relaxation times and proton scalar couplings of BPTI with values predicted by molecular dynamics. Journal of Magnetic Resonance. Series B. 104: 240-9. PMID 7520814 DOI: 10.1006/jmrb.1994.1081  0.84
1994 Beveridge DL, Ravishanker G. Molecular dynamics studies of DNA Current Opinion in Structural Biology. 4: 246-255. DOI: 10.1016/S0959-440X(94)90316-6  0.84
1994 Langley DR, Doyle TW, Beveridge DL. Probing the Underlying Basis for the Binding Specificity of Calicheamicin γ1I. A Molecular Dynamics Study Tetrahedron. 50: 1379-1396. DOI: 10.1016/S0040-4020(01)80625-6  0.84
1994 McConnell KJ, Nirmala R, Young MA, Ravishanker G, Beveridge DL. A nanosecond molecular dynamics trajectory for a B DNA double helix: Evidence for substates Journal of the American Chemical Society. 116: 4461-4462.  0.84
1994 Langley DR, Golik J, Krishnan B, Doyle TW, Beveridge DL. The DNA-esperamicin A1 complex. A model based on solvated molecular dynamics simulations Journal of the American Chemical Society. 116: 15-29.  0.84
1993 Prévost C, Louise-May S, Ravishanker G, Lavery R, Beveridge DL. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers. 33: 335-50. PMID 8461448 DOI: 10.1002/bip.360330303  0.84
1993 Vijayakumar S, Vishveshwara S, Ravishanker G, Beveridge DL. Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates. Biophysical Journal. 65: 2304-12. PMID 8312470 DOI: 10.1016/S0006-3495(93)81288-8  0.84
1993 Fritsch V, Ravishanker G, Beveridge DL, Westhof E. Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations. Biopolymers. 33: 1537-52. PMID 8218922 DOI: 10.1002/bip.360331005  0.84
1993 Subramanian PS, Beveridge DL. A Monte Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z form Theoretica Chimica Acta. 85: 3-15. DOI: 10.1007/BF01374572  0.84
1993 Harte WE, Beveridge DL. Mechanism for the destabilization of the dimer interface in a mutant HIV-1 protease: A molecular dynamics study Journal of the American Chemical Society. 115: 1231-1234.  0.84
1993 Harte WE, Beveridge DL. Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation Journal of the American Chemical Society. 115: 3883-3886.  0.84
1992 Withka JM, Swaminathan S, Srinivasan J, Beveridge DL, Bolton PH. Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities. Science (New York, N.Y.). 255: 597-9. PMID 1736362  0.84
1992 Harte WE, Swaminathan S, Beveridge DL. Molecular dynamics of HIV-1 protease. Proteins. 13: 175-94. PMID 1603808 DOI: 10.1002/prot.340130302  0.84
1992 Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophysical Journal. 63: 751-9. PMID 1384741 DOI: 10.1016/S0006-3495(92)81649-1  0.84
1991 Swaminathan S, Harte WE, Beveridge DL. Investigation of domain structure in protein via molecular dynamics simulation: Application to HIV-1 protease dimer Journal of the American Chemical Society. 113: 2717-2721.  0.84
1991 Jayaram B, Dicapua FM, Beveridge DL. A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ Represser-operator complex formation Journal of the American Chemical Society. 113: 5211-5215.  0.84
1991 Swaminathan S, Ravishanker G, Beveridge DL. Molecular dynamics of B-DNA including water and counterions: A 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field Journal of the American Chemical Society. 113: 5027-5040.  0.84
1991 Withka JM, Swaminathan S, Beveridge DL, Bolton PH. Time dependence of nuclear overhauser effects of duplex DNA from molecular dynamics trajectories Journal of the American Chemical Society. 113: 5041-5049.  0.84
1991 Jayaram B, Beveridge DL. Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: Excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions Journal of Physical Chemistry. 95: 2506-2516.  0.84
1991 DiCapua FM, Swaminathan S, Beveridge DL. Theoretical evidence for water insertion in α-helix bending: Molecular dynamics of gly30 and ala30 in vacuo and in solution Journal of the American Chemical Society. 113: 6145-6155.  0.84
1991 Langley DR, Doyle TW, Beveridge DL. The dynemicin-DNA intercalation complex. A model based on DNA affinity cleavage and molecular dynamics simulation Journal of the American Chemical Society. 113: 4395-4403.  0.84
1990 Subramanian PS, Pitchumani S, Beveridge DL, Berman HM. A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: comparison with crystallographic ordered water sites. Biopolymers. 29: 771-83. PMID 2383642 DOI: 10.1002/bip.360290411  0.84
1990 Subramanian PS, Swaminathan S, Beveridge DL. Theoretical account of the 'spine of hydration' in the minor groove of duplex d(CGCGAATTCGCG). Journal of Biomolecular Structure & Dynamics. 7: 1161-5. PMID 2361004 DOI: 10.1080/07391102.1990.10508553  0.84
1990 Harte WE, Swaminathan S, Mansuri MM, Martin JC, Rosenberg IE, Beveridge DL. Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. Proceedings of the National Academy of Sciences of the United States of America. 87: 8864-8. PMID 2247458  0.84
1990 Swaminathan S, Ravishanker G, Beveridge DL, Lavery R, Etchebest C, Sklenar H. Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI. Proteins. 8: 179-93. PMID 2235996 DOI: 10.1002/prot.340080208  0.84
1990 Srinivasan J, Withka JM, Beveridge DL. Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 3.0 force field. Biophysical Journal. 58: 533-47. PMID 2207251 DOI: 10.1016/S0006-3495(90)82397-3  0.84
1990 Jayaram B, Beveridge DL. Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions Journal of Physical Chemistry. 94: 4666-4671.  0.84
1990 Swaminathan S, Beveridge DL, Berman HM. Molecular dynamics simulation of a deoxydinucleoside-drug intercalation complex: dCpG/proflavin Journal of Physical Chemistry. 94: 4660-4665.  0.84
1990 DiCapua FM, Swaminathan S, Beveridge DL. Theoretical evidence for destabilization of an α-helix by water insertion: molecular dynamics of hydrated decaalanine Journal of the American Chemical Society. 112: 6768-6771.  0.84
1990 Jayaram B, Beveridge DL. A simple method to estimate free energy from a molecular simulation: Renormalization on the unit interval Journal of Physical Chemistry. 94: 7288-7293.  0.84
1990 Jayaram B, Swaminathan S, Beveridge DL, Sharp K, Honig B. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model Macromolecules. 23: 3156-3165.  0.84
1989 Subramanian PS, Beveridge DL. A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG): Monte Carlo simulation and comparison with crystallographic ordered water sites. Journal of Biomolecular Structure & Dynamics. 6: 1093-122. PMID 2684218 DOI: 10.1080/07391102.1989.10506539  0.84
1989 Beveridge DL, DiCapua FM. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annual Review of Biophysics and Biophysical Chemistry. 18: 431-92. PMID 2660832 DOI: 10.1146/annurev.bb.18.060189.002243  0.84
1989 Ravishanker G, Swaminathan S, Beveridge DL, Lavery R, Sklenar H. Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows. Journal of Biomolecular Structure & Dynamics. 6: 669-99. PMID 2619934 DOI: 10.1080/07391102.1989.10507729  0.84
1988 Jayaram B, Beveridge DL. Tanford-Kirkwood theory for concentric dielectric continua: application to dimethylphosphate. Biopolymers. 27: 616-27. PMID 3370297 DOI: 10.1002/bip.360270406  0.84
1988 Subramanian PS, Ravishanker G, Beveridge DL. Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation. Proceedings of the National Academy of Sciences of the United States of America. 85: 1836-40. PMID 3162310 DOI: 10.1073/pnas.85.6.1836  0.84
1988 Jayaram B, Mezei M, Beveridge DL. Conformational stability of dimethyl phosphate anion in water: Liquid-state free energy simulations Journal of the American Chemical Society. 110: 1691-1694.  0.84
1988 Jayaram B, Ravishanker G, Beveridge DL. Conformational preferences of phosphodiester torsion angles in dimethylphosphate anion in free space and water: Quasi-harmonic Monte Carlo and hydration shell calculations Journal of Physical Chemistry. 92: 1032-1034.  0.84
1986 Mezei M, Beveridge DL. Free energy simulations. Annals of the New York Academy of Sciences. 482: 1-23. PMID 3471099  0.84
1986 Mezei M, Beveridge DL. [2] Structural chemistry of biomolecular hydration via computer simulation: The proximity criterion Methods in Enzymology. 127: 21-47. DOI: 10.1016/0076-6879(86)27005-6  0.84
1985 Beveridge DL, Mezei M, Ravishanker G, Jayaram B. Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability Journal of Biosciences. 8: 167-178. DOI: 10.1007/BF02703974  0.84
1985 Ravishanker G, Beveridge DL. Potential of mean force for the stacking of phenyl rings in aqueous solution Journal of the American Chemical Society. 107: 2565-2566.  0.84
1985 Mezei M, Mehrotra PK, Beveridge DL. Monte Carlo determination of the free energy and internal energy of hydration for the Ala dipeptide at 25°C Journal of the American Chemical Society. 107: 2239-2245.  0.84
1984 Mezei M, Mehrotra PK, Beveridge DL. Monte Carlo computer simulation of the aqueous hydration of the glycine zwitterion at 25 degree C. Journal of Biomolecular Structure & Dynamics. 2: 1-27. PMID 6400925 DOI: 10.1080/07391102.1984.10507543  0.84
1984 Marchese FT, Beveridge DL. Cooperativity of hydrophillic and hydrophobic effects in the aqueous hydration of polyfunctional solutes Chemical Physics Letters. 105: 431-432. DOI: 10.1016/0009-2614(84)80056-1  0.84
1984 Marchese FT, Mehrotra PK, Beveridge DL. Monte Carlo study of the aqueous hydration of formamide at 25°C Journal of Physical Chemistry. 88: 5692-5702.  0.84
1984 Ravishanker G, Mehrotra PK, Mezei M, Beveridge DL. AQUEOUS HYDRATION OF BENZENE Journal of the American Chemical Society. 106: 4102-4108.  0.84
1983 Mezei M, Beveridge DL, Berman HM, Goodfellow JM, Finney JL, Neidle S. Monte Carlo studies on water in the dCpG/proflavin crystal hydrate. Journal of Biomolecular Structure & Dynamics. 1: 287-97. PMID 6400875 DOI: 10.1080/07391102.1983.10507440  0.84
1983 Mehrotra PK, Mezei M, Beveridge DL. Convergence acceleration in Monte Carlo computer simulation on water and aqueous solutions The Journal of Chemical Physics. 78: 3156-3166.  0.84
1982 Ravishanker G, Mezei M, Beveridge DL. Monte Carlo computer simulation study of the hydrophobic effect: Potential of mean force for [(CH4)2]aq at 25 and 50 °C Faraday Symposia of the Chemical Society. 17: 79-91. DOI: 10.1039/FS9821700079  0.84
1982 Mezei M, Beveridge DL. Further quasicomponent distribution function analysis of liquid water. Temperature dependence of the results The Journal of Chemical Physics. 76: 593-600.  0.84
1982 Marchese FT, Mehrotra PK, Beveridge DL. Transferable potential functions from quantum-mechanical calculations of intermolecular interaction energies Journal of Physical Chemistry. 86: 2592-2601.  0.84
1981 Mehrotra PK, Marchese FT, Beveridge DL. Statistical state solvation sites Journal of the American Chemical Society. 103: 672-673.  0.84
1981 Mezei M, Beveridge DL. Monte Carlo studies of the structure of dilute aqueous solutions of Li +, Na+, K+, F-, and Cl- The Journal of Chemical Physics. 74: 6902-6910.  0.84
1981 Marchese FT, Mehrotra PK, Beveridge DL. A revised potential function for the water dimer in the EPEN/2 form Journal of Physical Chemistry. 85: 1-3.  0.84
1980 Mehrotra PK, Beveridge DL. Structural analysis of molecular solutions based on quasi-component distribution functions. Application to [H2CO]aq at 25°C Journal of the American Chemical Society. 102: 4287-4294.  0.84
1980 Mezei M, Beveridge DL. Theoretical studies of hydrogen bonding in liquid water and dilute aqueous solutions The Journal of Chemical Physics. 74: 622-632.  0.84
1979 Klein ML, McDonald IR, Berne BJ, Rao M, Beveridge DL, Mehrotra PK. Radial correlations in associated liquids The Journal of Chemical Physics. 71: 3889-3891.  0.84
1979 Swaminathan S, Beveridge DL. Monte Carlo computer simulation of hydrophobic bonding [6] Journal of the American Chemical Society. 101: 5832-5833.  0.84
1979 Mezei M, Swaminathan S, Beveridge DL. Convergence characteristics of Monte Carlo-Metropolis computer simulations on liquid water The Journal of Chemical Physics. 71: 3366-3373.  0.84
1978 Schnuelle GW, Swaminathan S, Beveridge DL. A statistical thermodynamic supermolecule-continuum study of ion hydration: Cell and shell methods Theoretica Chimica Acta. 48: 17-27. DOI: 10.1007/BF00550237  0.84
1978 Swaminathan S, Harrison SW, Beveridge DL. Monte Carlo studies on the structure of a dilute aqueous solution of methane Journal of the American Chemical Society. 100: 5705-5712.  0.84
1978 Mezei M, Swaminathan S, Beveridge DL. Ab initio calculation of the free energy of liquid water [28] Journal of the American Chemical Society. 100: 3255-3256.  0.84
1977 Loesch HJ, Carley JS, Zandee L, Reuss J, Le Roy RJ, Child MS, Dixon DA, Herschbach DR, Klemperer W, Whitehead RJ, Swaminathan S, Guth E, Beveridge DL, Kutzelnigg W, Murrell JN, et al. General discussion Faraday Discussions of the Chemical Society. 62: 300-346. DOI: 10.1039/DC9776200300  0.84
1977 Swaminathan S, Beveridge DL. A theoretical study of the structure of liquid water based on quasi-component distribution functions Journal of the American Chemical Society. 99: 8392-8398.  0.84
1977 Swaminathan S, Whitehead RJ, Guth E, Beveridge DL. A heuristic intermolecular potential function for formaldehyde-water based on ab initio molecular orbital calculations Journal of the American Chemical Society. 99: 7817-7822.  0.84
1976 Harrison SW, Nolte HJ, Beveridge DL. Free energy of a charge distribution in a spheroidal cavity in a polarizable dielectric continuum Journal of Physical Chemistry. 80: 2580-2585.  0.84
1975 Beveridge DL, Schnuelle GW. Free energy of a charge distribution in concentric dielectric continua Journal of Physical Chemistry. 79: 2562-2566.  0.84
1975 Schnuelle GW, Beveridge DL. A statistical thermodynamic supermolecule-continuum study of ion hydration. I. Site method Journal of Physical Chemistry. 79: 2566-2573.  0.84
1974 Beveridge DL, Kelly MM, Radna RJ. A theoretical study of solvent effects on the conformational stability of acetylcholine. Journal of the American Chemical Society. 96: 3769-78. PMID 4850350  0.84
1974 Beveridge DL, Schnuelle GW. Statistical thermodynamic consideration of solvent effects on conformational stability. The supermolecule-continuum model Journal of Physical Chemistry. 78: 2064-2069.  0.84
1973 Radna RJ, Beveridge DL, Bender AL. Structural chemistry of cholinergic neural transmission systems. II. A quantum theoretical study of the molecular electronic structure of muscarine, nicotine, acetyl- -methylcholine, acetyl- -methylcholine, acetyl- , -dimethylcholine, and further studies on acetylcholine. Journal of the American Chemical Society. 95: 3831-46. PMID 4710055  0.84
1973 Beveridge DL, Wun W. A comparison of the photoelectron spectrum and crystal orbital calculations of polyethylene Chemical Physics Letters. 18: 570-571. DOI: 10.1016/0009-2614(73)80467-1  0.84
1972 Beveridge DL, Jano I, Ladik J. INDO and MINDO/2 crystal orbital study of polyacetylene, polyethylene, and polyglycine The Journal of Chemical Physics. 56: 4744-4751.  0.84
1971 Beveridge DL, Radna RJ. Structural chemistry of cholinergic neural transmission systems. I. A quantum theoretical study of the molecular electronic structure of acetylcholine. Journal of the American Chemical Society. 93: 3759-64. PMID 4326331  0.84
1971 Kang S, Beveridge DL. Molecular orbital aspects of substituent effects Theoretica Chimica Acta. 22: 312-314. DOI: 10.1007/BF00530278  0.84
1971 Beveridge DL, Mciver JW. INDO Molecular orbital study of hyperfine tensors: Theory, methodology, and applications to CH, CH3, and radicaloid derivatives of malonic acid The Journal of Chemical Physics. 54: 4675-4680.  0.84
1971 Beveridge DL, Hinze J. Parametrization of semiempirical π-electron molecular orbital calculations, π Systems containing carbon, nitrogen, oxygen, and fluorine Journal of the American Chemical Society. 93: 3107-3114.  0.84
1971 Beveridge DL, Guth E. Quantum theoretical considerations of the ortho:para ratio for proton isotropic hyperfine coupling constants in benzyl radical The Journal of Chemical Physics. 55: 458.  0.84
1971 Bulkin BJ, Prochaska FT, Beveridge DL. Raman spectrum and quantum chemical study of the equilibrium geometry of p-azoxydianisole The Journal of Chemical Physics. 55: 5828-5829.  0.84
1971 Beveridge DL, Bulkin BJ. Descriptive crystal orbital theory of conduction in diamond and graphite Journal of Chemical Education. 48: 587-590.  0.84
1969 Beveridge DL, McIver JW. INDO molecular orbital calculation of anisotropic hyperfine coupling constants Chemical Physics Letters. 4: 126-128.  0.84
1968 Beveridge DL, Miller K. An INDO-molecular orbital study of vibronic effects in isotopically substituted methyl radicals Molecular Physics. 14: 401-412. DOI: 10.1080/00268976800100511  0.84
1968 Pople JA, Beveridge DL. Delocalization of Unpaired Electron Density of [formula omitted] Radicals into Substituent Phenyl Groups Journal of Chemical Physics. 49: 4725-4726. DOI: 10.1063/1.1669945  0.84
1968 Beveridge DL, Dobosh PA, Popie JA. Molecular-orbital theory of geometry and hyperfine coupling constants of fluorinated methyl radicals The Journal of Chemical Physics. 48: 4802-4803.  0.84
1968 Pople JA, Beveridge DL. Delocalization of unpaired electron density of Π radicals into substituent phenyl groups The Journal of Chemical Physics. 49: 4720-4721.  0.84
1968 Pople JA, Beveridge DL, Dobosh PA. Molecular orbital theory of the electronic structure of organic compounds. II. Spin densities in paramagnetic species Journal of the American Chemical Society. 90: 4201-4209.  0.84
1967 Pople JA, Beveridge DL, Dobosh PA. Approximate self-consistent molecular-orbital theory. V. Intermediate neglect of differential overlap The Journal of Chemical Physics. 47: 2026-2033.  0.84
1967 Jaffé HH, Beveridge DL, Orchin M. Understanding ultraviolet spectra of organic molecules: Some limitations on the use of orbital energy level diagrams Journal of Chemical Education. 44: 383-386.  0.84
1966 Beveridge DL, Jaffé HH. The electronic structure and spectra of cis-and trans-azobenzene Journal of the American Chemical Society. 88: 1948-1953.  0.84
1965 Beveridge DL, Jaffé HH. The electronic structure and spectra of cis- and trans-stilbene. Journal of the American Chemical Society. 87: 5340-6. PMID 5844820  0.84
1964 Jaffé HH, Beveridge DL, Jones HL. Excited state pK's. I. Azobenzene and azoxybenzene [1] Journal of the American Chemical Society. 86: 2932-2934.  0.84
1964 Jones HL, Beveridge DL. Lone pair interaction in the Chichibabin reaction Tetrahedron Letters. 5: 1577-1583.  0.84
Low-probability matches
1995 Beveridge DL, Hilbers CW, Kallenbach NR, Lille DMJ, Olson WK, Shakked Z, Redfield AG, Rich A, Sarma RH. Ninth conversation in the discipline biomolecular stereodynamics the university, albany, new york, june 20-24, 1995 Journal of Biomolecular Structure and Dynamics. 12: iv-viii. DOI: 10.1080/07391102.1995.10508771  0.2
1984 Beveridge DL, Maye PV, Jayaram B, Ravishanker G, Mezei M. Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies. Journal of Biomolecular Structure & Dynamics. 2: 261-70. PMID 6401130 DOI: 10.1080/07391102.1984.10507565  0.2
1986 Mezei M, Beveridge DL. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. Methods in Enzymology. 127: 21-47. PMID 3755494  0.12
1982 Jolicoeur C, Tucker EE, Ben-Naim A, Symons MCR, McKenna J, Christian SD, Franks F, Lilley TH, Engberts JBFN, Linse P, Kleeberg H, Zeidler MD, Berendsen HJC, Yarwood J, Weingärtner H, ... ... Beveridge DL, et al. General discussion Faraday Symposia of the Chemical Society. 17: 175-229. DOI: 10.1039/FS9821700175  0.04
1998 Beveridge DL. Truly a team effort. Axone (Dartmouth, N.S.). 20: 34-8. PMID 10196877  0.01
1995 Beveridge DL. Back to basics. Axone (Dartmouth, N.S.). 17: 6-8. PMID 7654598  0.01
1990 Beveridge DL, Hilbers CW, Kallenbach NR, Redfield AG, Rich A, Sarma RH, Seeman NC, Wang AH. Seventh conversation in the discipline biomolecular stereodynamics state university of new york at albany, june 18·22, 1991 Journal of Biomolecular Structure and Dynamics. 8: viii-xii. DOI: 10.1080/07391102.1990.10507820  0.01
1968 Beveridge DL, Miller K. An INDO MO orbital study of vibronic effects in isotopically substituted methyl radicals Molecular Physics. 15: 332. DOI: 10.1080/00268976800101161  0.01
Hide low-probability matches.