Year |
Citation |
Score |
2023 |
Jayaraj A, Thayer KM, Beveridge DL, Hingorani MM. Molecular Dynamics of Mismatch Detection - How MutS Uses Indirect Readout to Find Errors in DNA. Biophysical Journal. PMID 37329136 DOI: 10.1016/j.bpj.2023.06.006 |
0.741 |
|
2023 |
Cowan BS, Beveridge DL, Thayer KM. Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis. The Journal of Physical Chemistry. B. PMID 36626697 DOI: 10.1021/acs.jpcb.2c06546 |
0.682 |
|
2021 |
Jasuja R, Spencer D, Jayaraj A, Peng L, Krishna M, Lawney B, Patel P, Jayaram B, Thayer KM, Beveridge DL, Bhasin S. Estradiol induces allosteric coupling and partitioning of sex-hormone-binding globulin monomers among conformational states. Iscience. 24: 102414. PMID 34041454 DOI: 10.1016/j.isci.2021.102414 |
0.743 |
|
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 |
0.752 |
|
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 |
0.779 |
|
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 |
0.732 |
|
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 |
0.762 |
|
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 |
0.366 |
|
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 |
0.647 |
|
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 |
0.627 |
|
2013 |
Nocka LM, Mukerji I, Beveridge D, Wheatley L. Structure and Function of Holliday Junctions Complexed with Ions and HU Protein Biophysical Journal. 104: 75a. DOI: 10.1016/J.Bpj.2012.11.454 |
0.428 |
|
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 |
0.498 |
|
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 |
0.49 |
|
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 |
0.491 |
|
2012 |
Mukerji I, Vitoc CI, Litke J, Wheatley E, Buzovetsky O, Li Y, Beveridge DL. Structure of DNA Four-Way Junctions: Effect of Ions and Proteins Biophysical Journal. 102: 75a. DOI: 10.1016/J.Bpj.2011.11.440 |
0.425 |
|
2012 |
Wheatley E, Mukerji I, Beveridge DL. Structure Prediction of an Unusual Protein-DNA Complex Hu with a DNA Four-Way Junction Biophysical Journal. 102: 71a. DOI: 10.1016/J.Bpj.2011.11.414 |
0.485 |
|
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. |
0.327 |
|
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 |
0.467 |
|
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 |
0.725 |
|
2011 |
Pieniazek SN, Hingorani MM, Beveridge DL. Allosterism in Muts Proteins: How DNA Mismatch Recognition Signals Repair Biophysical Journal. 100: 535a. DOI: 10.1016/J.Bpj.2010.12.3121 |
0.425 |
|
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 |
0.667 |
|
2010 |
Pieniazek SN, Bhattacharyya M, Vishveshwara S, Hingorani M, Beveridge DL. Recognition and Signaling in DNA Mismatch Repair: Interdomain Communication in T. Aquaticus Muts Proteins Biophysical Journal. 98: 568a-569a. DOI: 10.1016/J.Bpj.2009.12.3084 |
0.438 |
|
2010 |
Wheatley E, Beveridge DL, Pieniazek S. A Molecular Dynamics Study of DNA Bending in the IHF-DNA Complex Biophysical Journal. 98: 470a. DOI: 10.1016/J.Bpj.2009.12.2559 |
0.47 |
|
2010 |
BEVERIDGE DL, MCCONNELL KJ, NIRMALA R, YOUNG MA. ChemInform Abstract: Molecular Dynamics Simulation of DNA and Protein-DNA Complexes Including Solvent. Recent Progress. Cheminform. 26: no-no. DOI: 10.1002/chin.199509325 |
0.669 |
|
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 |
0.802 |
|
2009 |
Pieniazek SN, Hingorani M, Beveridge DL. Recognition and Signaling in DNA Mismatch Repair: MD Studies of MutS Complexes with DNA and ATP Biophysical Journal. 96: 64a. DOI: 10.1016/J.Bpj.2008.12.229 |
0.453 |
|
2009 |
Pople JA, Beveridge DL, Ostlund NS. Recent progress in approximate self-consistent-field theory International Journal of Quantum Chemistry. 1: 293-305. DOI: 10.1002/QUA.560010635 |
0.352 |
|
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 |
0.631 |
|
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 |
0.788 |
|
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 |
0.724 |
|
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 |
0.719 |
|
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 |
0.734 |
|
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 |
0.731 |
|
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 |
0.802 |
|
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 |
0.462 |
|
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 |
0.721 |
|
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 |
0.723 |
|
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 |
0.772 |
|
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 |
0.459 |
|
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 |
0.479 |
|
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 |
0.477 |
|
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 |
0.807 |
|
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 |
0.764 |
|
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 |
0.763 |
|
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 |
0.503 |
|
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 |
0.67 |
|
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 |
0.416 |
|
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 |
0.765 |
|
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 |
0.765 |
|
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 |
0.74 |
|
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 |
0.789 |
|
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 |
0.7 |
|
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 |
0.823 |
|
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 |
0.645 |
|
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 |
0.741 |
|
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 |
0.689 |
|
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 |
0.788 |
|
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 |
0.687 |
|
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 |
0.765 |
|
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 |
0.356 |
|
1999 |
Manoj N, Srinivas VR, Surolia A, Vijayan M, Suguna K, Ravishankar R, Schwarzenbacher R, Zeth K, Diederichs, Kostner GM, Gries A, Laggner P, Prassl R, Madhusudan, Akamine P, ... ... Beveridge DL, et al. Contributory presentations/posters Journal of Biosciences. 24: 33-198. DOI: 10.1007/Bf02989373 |
0.554 |
|
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 |
0.762 |
|
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. DOI: 10.1002/(Sici)1097-461X(1999)75:3<313::Aid-Qua20>3.0.Co;2-L |
0.757 |
|
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 |
0.461 |
|
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. DOI: 10.1021/Jp9823188 |
0.647 |
|
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. DOI: 10.1021/Jp982007X |
0.634 |
|
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. DOI: 10.1021/Jp980548G |
0.434 |
|
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 |
0.665 |
|
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. |
0.383 |
|
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 |
0.525 |
|
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 |
0.503 |
|
1997 |
Beveridge DL. Monte Carlo and Molecular Dynamics Simulations in Polymer Science Edited by Kurt Binder (Johannes-Gutenberg University). Oxford University Press: New York, Oxford, 1995. xiv + 587 pp. $95.00. ISBN 0-19-509438-7. Journal of the American Chemical Society. 119: 9938-9938. DOI: 10.1021/Ja965637Q |
0.311 |
|
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 |
0.663 |
|
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. DOI: 10.1002/9780470125885.Ch6 |
0.611 |
|
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 |
0.621 |
|
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 |
0.44 |
|
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 |
0.431 |
|
1995 |
Vijayakumar S, Ravishanker G, Pratt RF, Beveridge DL. Molecular Dynamics Simulation of a Class A .beta.-Lactamase: Structural and Mechanistic Implications Journal of the American Chemical Society. 117: 1722-1730. DOI: 10.1021/Ja00111A008 |
0.339 |
|
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 |
0.345 |
|
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 |
0.721 |
|
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 |
0.365 |
|
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 |
0.376 |
|
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. DOI: 10.1021/Ja00089A039 |
0.689 |
|
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. DOI: 10.1021/Ja00080A003 |
0.474 |
|
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 |
0.481 |
|
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 |
0.396 |
|
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: 10.1016/0263-7855(92)80019-A |
0.442 |
|
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 |
0.447 |
|
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. DOI: 10.1021/Ja00063A005 |
0.328 |
|
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. DOI: 10.1021/Ja00057A003 |
0.341 |
|
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 |
0.37 |
|
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 |
0.341 |
|
1992 |
Harte WE, Swaminathan S, Beveridge DL. Molecular dynamics of HIV-1 protease. Proteins. 13: 175-94. PMID 1603808 DOI: 10.1002/Prot.340130302 |
0.432 |
|
1991 |
DiCapua FM, Swaminathan S, Beveridge DL. Theoretical evidence for water insertion in .alpha.-helix bending: molecular dynamics of Gly30 and Ala30 in vacuo and in solution Journal of the American Chemical Society. 113: 6145-6155. DOI: 10.1021/Ja00016A034 |
0.348 |
|
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 .lambda. repressor-operator complex formation Journal of the American Chemical Society. 113: 5211-5215. DOI: 10.1021/Ja00014A011 |
0.641 |
|
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. DOI: 10.1021/Ja00013A044 |
0.419 |
|
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. DOI: 10.1021/Ja00013A043 |
0.397 |
|
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. DOI: 10.1021/Ja00012A004 |
0.462 |
|
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. DOI: 10.1021/Ja00007A054 |
0.356 |
|
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. |
0.322 |
|
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 |
0.372 |
|
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 |
0.383 |
|
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 DOI: 10.1073/Pnas.87.22.8864 |
0.373 |
|
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 |
0.437 |
|
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 |
0.425 |
|
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. DOI: 10.1021/Ma00214A021 |
0.702 |
|
1990 |
DiCapua FM, Swaminathan S, Beveridge DL. Theoretical evidence for destabilization of an .alpha.-helix by water insertion: molecular dynamics of hydrated decaalanine Journal of the American Chemical Society. 112: 6768-6771. DOI: 10.1021/Ja00175A004 |
0.37 |
|
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. DOI: 10.1021/J100374A054 |
0.354 |
|
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. |
0.302 |
|
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 |
0.478 |
|
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 |
0.56 |
|
1988 |
Berman HM, Sowri A, Ginel S, Beveridge D. A systematic study of patterns of hydrationin nucleic acids:(i) guanine and cytosine Journal of Biomolecular Structure and Dynamics. 5: 1101-1110. PMID 3271499 DOI: 10.1080/07391102.1988.10506451 |
0.335 |
|
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 |
0.462 |
|
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. DOI: 10.1021/Ja00214A005 |
0.604 |
|
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. DOI: 10.1021/J100316A009 |
0.579 |
|
1987 |
Jayaram B, Mezei M, Beveridge DL. Monte Carlo study of the aqueous hydration of dimethylphosphate conformations Journal of Computational Chemistry. 8: 917-942. DOI: 10.1002/Jcc.540080702 |
0.399 |
|
1986 |
Mezei M, Beveridge DL. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. Methods in Enzymology. 127: 21-47. PMID 3755494 DOI: 10.1016/0076-6879(86)27005-6 |
0.426 |
|
1986 |
Mezei M, Beveridge DL. Free energy simulations. Annals of the New York Academy of Sciences. 482: 1-23. PMID 3471099 DOI: 10.1111/J.1749-6632.1986.Tb20933.X |
0.337 |
|
1986 |
Marchese FT, Beveridge DL. Thermal motion from monte carlo simulations of aqueous ionic solutions International Journal of Quantum Chemistry. 29: 619-625. DOI: 10.1002/Qua.560290405 |
0.337 |
|
1986 |
Ravishanker G, Mezei M, Beveridge DL. Conformational stability and flexibility of the ala dipeptide in free space and water: Monte Carlo computer simulation studies Journal of Computational Chemistry. 7: 345-348. DOI: 10.1002/Jcc.540070311 |
0.353 |
|
1986 |
Mezei M, Harrison SW, Ravishanker G, Beveridge DL. Monte Carlo Studies of the Aqueous Hydration ofcis- andtrans-N- Methyl-Acetamide: Sensitivity of Results to Convergence and to Choice of Intermolecular Potential Functions Israel Journal of Chemistry. 27: 163-172. DOI: 10.1002/Ijch.198600025 |
0.373 |
|
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 |
0.39 |
|
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 |
0.647 |
|
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 |
0.347 |
|
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 |
0.312 |
|
1984 |
Mehrotra PK, Mezei M, Beveridge DL. Monte Carlo determination of the internal energies of hydration for the Ala dipeptide in the C7, C5, ?R, and PII conformations International Journal of Quantum Chemistry. 26: 301-308. DOI: 10.1002/Qua.560260731 |
0.335 |
|
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 |
0.392 |
|
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. DOI: 10.1063/1.445231 |
0.316 |
|
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. DOI: 10.1063/1.442707 |
0.342 |
|
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 |
0.37 |
|
1981 |
Mezei M, Beveridge DL. Monte Carlo studies of the structure of dilute aqueous sclutions of Li+, Na+, K+, F−, and Cl− Journal of Chemical Physics. 74: 6902-6910. DOI: 10.1063/1.441101 |
0.368 |
|
1980 |
Swaminathan S, Beveridge DL. Monte Carlo computer simulation of hydrophobic bonding Cheminform. 11. DOI: 10.1002/Chin.198001093 |
0.323 |
|
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. DOI: 10.1063/1.438725 |
0.354 |
|
1979 |
Swaminathan S, Beveridge DL. Monte Carlo computer simulation of hydrophobic bonding Journal of the American Chemical Society. 101: 5832-5833. DOI: 10.1021/Ja00513A065 |
0.323 |
|
1978 |
Mezei M, Swaminathan S, Beveridge DL. Ab initio calculation of the free energy of liquid water Journal of the American Chemical Society. 100: 3255-3256. DOI: 10.1021/Ja00478A070 |
0.303 |
|
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 |
0.334 |
|
1978 |
Harrison SW, Swaminathan S, Beveridge DL, Ditchfield R. Heuristic intermolecular potential function for the methane-water interaction based onab initio quantum-mechanical calculations International Journal of Quantum Chemistry. 14: 319-327. DOI: 10.1002/Qua.560140310 |
0.321 |
|
1978 |
Mezei M, Swaminathan S, Beveridge DL. Ab initio calculation of the free energy of liquid water Cheminform. 9. DOI: 10.1002/Chin.197832020 |
0.303 |
|
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. DOI: 10.1021/Ja00466A011 |
0.326 |
|
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. DOI: 10.1021/J100613A015 |
0.308 |
|
1971 |
Hinze J, Beveridge DL. Parametrization of semiempirical .pi.-electron molecular orbital calculations. .pi.Systems containing carbon, nitrogen, oxygen, and fluorine Journal of the American Chemical Society. 93: 3107-3114. DOI: 10.1021/Ja00742A002 |
0.526 |
|
1971 |
Beveridge DL. Chemical Systems: Energetics, Dynamics, Structure(Campell, J.A.) Journal of Chemical Education. 48: A560. DOI: 10.1021/Ed048Pa560.1 |
0.313 |
|
1971 |
BEVERIDGE DL, HINZE J. ChemInform Abstract: PARAMETRISIERUNG HALBEMPIRISCHER PI-ELEKTRON-MO-BERECHNUNGEN, KOHLENSTOFF, STICKSTOFF, SAUERSTOFF UND FLUOR ENTHALTENDE PI-SYST. Chemischer Informationsdienst. Organische Chemie. 2: no-no. DOI: 10.1002/Chin.197138085 |
0.487 |
|
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. |
0.477 |
|
1969 |
Beveridge DL, McIver JW. INDO molecular orbital calculation of anisotropic hyperfine coupling constants Chemical Physics Letters. 4: 126-128. DOI: 10.1016/0009-2614(69)80074-6 |
0.307 |
|
1968 |
Beveridge DL, Dobosh PA, Pople JA. Molecular‐Orbital Theory of Geometry and Hyperfine Coupling Constants of Fluorinated Methyl Radicals The Journal of Chemical Physics. 48: 4802-4803. DOI: 10.1063/1.1668077 |
0.368 |
|
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. DOI: 10.1021/JA01018A003 |
0.379 |
|
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. DOI: 10.1063/1.1712233 |
0.355 |
|
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. |
0.489 |
|
1966 |
Beveridge DL, Jaffé HH. The electronic structure and spectra of cis-and trans-azobenzene Journal of the American Chemical Society. 88: 1948-1953. |
0.469 |
|
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 DOI: 10.1021/Ja00951A014 |
0.522 |
|
1964 |
Jaffe HH, Beveridge DL, Jones HL. Excited State pK's. Azobenzene and Azoxybenzene Journal of the American Chemical Society. 86: 2932-2934. DOI: 10.1021/Ja01068A033 |
0.492 |
|
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. |
0.436 |
|
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