| Year |
Citation |
Score |
| 2009 |
Andrea TA, Jorgensen EC, Kollman PA. Differentiation of D- and L-Thyroxine by the plasma protein prealbumin International Journal of Quantum Chemistry. 14: 191-200. DOI: 10.1002/Qua.560140720 |
0.321 |
|
| 2009 |
Pendergast P, Hayes EF, Liedtke RC, Schwartz ME, Rothenberg S, Kollman PA. MOLE: a system for quantum chemistry. II. Recent developments International Journal of Quantum Chemistry. 10: 77-83. DOI: 10.1002/Qua.560100807 |
0.306 |
|
| 2006 |
Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. New-generation amber united-atom force field. The Journal of Physical Chemistry. B. 110: 13166-76. PMID 16805629 DOI: 10.1021/Jp060163V |
0.535 |
|
| 2006 |
Beà I, Gotsev MG, Ivanov PM, Jaime C, Kollman PA. Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study. The Journal of Organic Chemistry. 71: 2056-63. PMID 16496993 DOI: 10.1021/Jo052469O |
0.303 |
|
| 2006 |
Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling. 25: 247-60. PMID 16458552 DOI: 10.1016/J.Jmgm.2005.12.005 |
0.546 |
|
| 2006 |
Minehardt TJ, Kollman PA, Cooke R, Pate E. The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin. Biophysical Journal. 90: 2445-9. PMID 16428279 DOI: 10.1529/Biophysj.105.072900 |
0.306 |
|
| 2005 |
Wang J, Kang X, Kuntz ID, Kollman PA. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. Journal of Medicinal Chemistry. 48: 2432-44. PMID 15801834 DOI: 10.1021/Jm049606E |
0.632 |
|
| 2004 |
Kuhn B, Kollman PA, Stahl M. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. Journal of Computational Chemistry. 25: 1865-72. PMID 15376253 DOI: 10.1002/Jcc.20111 |
0.641 |
|
| 2004 |
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. Journal of Computational Chemistry. 25: 1157-74. PMID 15116359 DOI: 10.1002/Jcc.20035 |
0.566 |
|
| 2004 |
Wen EZ, Hsieh MJ, Kollman PA, Luo R. Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. Journal of Molecular Graphics & Modelling. 22: 415-24. PMID 15099837 DOI: 10.1016/J.Jmgm.2003.12.008 |
0.376 |
|
| 2003 |
Masukawa KM, Kollman PA, Kuntz ID. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. Journal of Medicinal Chemistry. 46: 5628-37. PMID 14667217 DOI: 10.1021/Jm030060Q |
0.612 |
|
| 2003 |
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 24: 1999-2012. PMID 14531054 DOI: 10.1002/Jcc.10349 |
0.569 |
|
| 2003 |
Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA. Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. Journal of Computational Chemistry. 24: 1371-7. PMID 12868101 DOI: 10.1002/Jcc.10293 |
0.773 |
|
| 2003 |
Gouda H, Kuntz ID, Case DA, Kollman PA. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers. 68: 16-34. PMID 12579577 DOI: 10.1002/Bip.10270 |
0.607 |
|
| 2003 |
Alagona G, Ghio C, Kollman PA. The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach. Journal of Computational Chemistry. 24: 46-56. PMID 12483674 DOI: 10.1002/Jcc.10153 |
0.337 |
|
| 2003 |
Kollman PA, Case DA. Drug-Target Binding Forces: Advances in Force Field Approaches Burger's Medicinal Chemistry and Drug Discovery. 169-185. DOI: 10.1002/0471266949.Bmc004 |
0.363 |
|
| 2002 |
Asada T, Gouda H, Kollman PA. Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement. Journal of the American Chemical Society. 124: 12535-42. PMID 12381197 DOI: 10.1021/Ja020774A |
0.363 |
|
| 2002 |
Bürgi R, Kollman PA, Van Gunsteren WF. Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. Proteins. 47: 469-80. PMID 12001225 DOI: 10.1002/Prot.10046 |
0.347 |
|
| 2002 |
Mooney SD, Kollman PA, Klein TE. Conformational preferences of substituted prolines in the collagen triple helix. Biopolymers. 64: 63-71. PMID 11979516 DOI: 10.1002/Bip.10123 |
0.301 |
|
| 2002 |
Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. Journal of Computational Chemistry. 23: 15-27. PMID 11913381 DOI: 10.1002/Jcc.1153 |
0.391 |
|
| 2002 |
Huo S, Wang J, Cieplak P, Kollman PA, Kuntz ID. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. Journal of Medicinal Chemistry. 45: 1412-9. PMID 11906282 DOI: 10.1021/Jm010338J |
0.701 |
|
| 2002 |
Dixon RW, Radmer RJ, Kuhn B, Kollman PA, Yang J, Raposo C, Wilcox CS, Klumb LA, Stayton PS, Behnke C, Le Trong I, Stenkamp R. Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin. The Journal of Organic Chemistry. 67: 1827-37. PMID 11895399 DOI: 10.1021/Jo991846S |
0.628 |
|
| 2002 |
Minehardt TJ, Marzari N, Cooke R, Pate E, Kollman PA, Car R. A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophysical Journal. 82: 660-75. PMID 11806909 DOI: 10.1016/S0006-3495(02)75429-5 |
0.355 |
|
| 2002 |
Kollman PA, Kuhn B, Peräkylä M. Computational studies of enzyme-catalyzed reactions: Where are we in predicting mechanisms and in understanding the nature of enzyme catalysis? Journal of Physical Chemistry B. 106: 1537-1542. DOI: 10.1021/Jp012017P |
0.337 |
|
| 2002 |
Wang J, Wang W, Huo S, Lee M, Kollman PA. Solvation model based on weighted solvent accessible surface area Journal of Physical Chemistry B. 105: 5055-5067. DOI: 10.1021/Jp0102318 |
0.302 |
|
| 2002 |
Beà I, Jaime C, Kollman P. Molecular recognition by β-cyclodextrin derivatives: Molecular dynamics, free-energy perturbation and molecular mechanics/Poisson-Boltzmann surface area goals and problems Theoretical Chemistry Accounts. 108: 286-292. DOI: 10.1007/S00214-002-0384-4 |
0.366 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: electrostatics and solvation. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.9. PMID 18428877 DOI: 10.1002/0471142700.Nc0709S05 |
0.655 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: energy and sampling. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.8. PMID 18428876 DOI: 10.1002/0471142700.Nc0708S04 |
0.695 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.5. PMID 18428873 DOI: 10.1002/0471142700.Nc0705S06 |
0.652 |
|
| 2001 |
Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: setup and analysis. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.10. PMID 18428869 DOI: 10.1002/0471142700.Nc0710S06 |
0.672 |
|
| 2001 |
Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. Journal of Molecular Biology. 313: 417-30. PMID 11800566 DOI: 10.1006/Jmbi.2001.5032 |
0.372 |
|
| 2001 |
Wang W, Kollman PA. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proceedings of the National Academy of Sciences of the United States of America. 98: 14937-42. PMID 11752442 DOI: 10.1073/Pnas.251265598 |
0.354 |
|
| 2001 |
Lee TS, Chong LT, Chodera JD, Kollman PA. An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. Journal of the American Chemical Society. 123: 12837-48. PMID 11749542 DOI: 10.1021/Ja011096F |
0.7 |
|
| 2001 |
Lee MR, Kollman PA. Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. Structure (London, England : 1993). 9: 905-16. PMID 11591346 DOI: 10.1016/S0969-2126(01)00660-8 |
0.419 |
|
| 2001 |
Krueger BP, Kollman PA. Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship. Proteins. 45: 4-15. PMID 11536355 DOI: 10.1002/Prot.1118 |
0.746 |
|
| 2001 |
Wang J, Morin P, Wang W, Kollman PA. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. Journal of the American Chemical Society. 123: 5221-30. PMID 11457384 DOI: 10.1021/Ja003834Q |
0.43 |
|
| 2001 |
Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. Journal of the American Chemical Society. 123: 3986-94. PMID 11457149 DOI: 10.1021/Ja003164O |
0.451 |
|
| 2001 |
Lee MR, Baker D, Kollman PA. 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. Journal of the American Chemical Society. 123: 1040-6. PMID 11456657 DOI: 10.1021/Ja003150I |
0.354 |
|
| 2001 |
Kuhn B, Jacobsen W, Christians U, Benet LZ, Kollman PA. Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. Journal of Medicinal Chemistry. 44: 2027-34. PMID 11384247 DOI: 10.1021/Jm010079Y |
0.596 |
|
| 2001 |
Lee MR, Duan Y, Kollman PA. State of the art in studying protein folding and protein structure prediction using molecular dynamics methods. Journal of Molecular Graphics & Modelling. 19: 146-9. PMID 11381525 DOI: 10.1016/S1093-3263(00)00126-1 |
0.356 |
|
| 2001 |
Reyes CM, Nifosì R, Frankel AD, Kollman PA. Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophysical Journal. 80: 2833-42. PMID 11371457 DOI: 10.1016/S0006-3495(01)76250-9 |
0.577 |
|
| 2001 |
Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annual Review of Biophysics and Biomolecular Structure. 30: 211-43. PMID 11340059 DOI: 10.1146/Annurev.Biophys.30.1.211 |
0.619 |
|
| 2001 |
Wang L, Duan Y, Stouten P, De Lucca GV, Klabe RM, Kollman PA. Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. Journal of Computer-Aided Molecular Design. 15: 145-56. PMID 11272701 DOI: 10.1023/A:1008156222963 |
0.322 |
|
| 2001 |
Minehardt TJ, Cooke R, Pate E, Kollman PA. Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd. Biophysical Journal. 80: 1151-68. PMID 11222280 DOI: 10.1016/S0006-3495(01)76092-4 |
0.397 |
|
| 2001 |
Kollman PA, Kuhn B, Donini O, Perakyla M, Stanton R, Bakowies D. Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. Accounts of Chemical Research. 34: 72-9. PMID 11170358 DOI: 10.1021/Ar000032R |
0.602 |
|
| 2001 |
Mooney SD, Huang CC, Kollman PA, Klein TE. Computed free energy differences between point mutations in a collagen-like peptide. Biopolymers. 58: 347-53. PMID 11169394 DOI: 10.1002/1097-0282(200103)58:3<347::Aid-Bip1011>3.0.Co;2-M |
0.334 |
|
| 2001 |
Wang J, Kollman PA. Automatic parameterization of force field by systematic search and genetic algorithms Journal of Computational Chemistry. 22: 1219-1228. DOI: 10.1002/Jcc.1079 |
0.325 |
|
| 2001 |
Cieplak P, Caldwell J, Kollman P. Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases Journal of Computational Chemistry. 22: 1048-1057. DOI: 10.1002/Jcc.1065 |
0.414 |
|
| 2000 |
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J |
0.813 |
|
| 2000 |
Nifosì R, Reyes CM, Kollman PA. Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. Nucleic Acids Research. 28: 4944-55. PMID 11121486 DOI: 10.1093/Nar/28.24.4944 |
0.618 |
|
| 2000 |
Donini OA, Kollman PA. Calculation and prediction of binding free energies for the matrix metalloproteinases. Journal of Medicinal Chemistry. 43: 4180-8. PMID 11063614 DOI: 10.1021/Jm000040D |
0.322 |
|
| 2000 |
Wang W, Kollman PA. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. Journal of Molecular Biology. 303: 567-82. PMID 11054292 DOI: 10.1006/Jmbi.2000.4057 |
0.376 |
|
| 2000 |
Cheatham TE, Kollman PA. Molecular dynamics simulation of nucleic acids. Annual Review of Physical Chemistry. 51: 435-71. PMID 11031289 DOI: 10.1146/Annurev.Physchem.51.1.435 |
0.618 |
|
| 2000 |
Pitera JW, Kollman PA. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins. 41: 385-97. PMID 11025549 DOI: 10.1002/1097-0134(20001115)41:3<385::Aid-Prot100>3.0.Co;2-R |
0.713 |
|
| 2000 |
Kuhn B, Kollman PA. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. Journal of Medicinal Chemistry. 43: 3786-91. PMID 11020294 DOI: 10.1021/Jm000241H |
0.661 |
|
| 2000 |
Lee MR, Duan Y, Kollman PA. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins. 39: 309-16. PMID 10813813 DOI: 10.1002/(Sici)1097-0134(20000601)39:4<309::Aid-Prot40>3.0.Co;2-S |
0.413 |
|
| 2000 |
Reyes CM, Kollman PA. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. Journal of Molecular Biology. 297: 1145-58. PMID 10764579 DOI: 10.1006/Jmbi.2000.3629 |
0.627 |
|
| 2000 |
Reyes CM, Kollman PA. Investigating the binding specificity of U1A-RNA by computational mutagenesis. Journal of Molecular Biology. 295: 1-6. PMID 10623503 DOI: 10.1006/Jmbi.1999.3319 |
0.574 |
|
| 2000 |
Lee TS, Massova I, Kuhn B, Kollman PA. QM and WM-FE simulations on reactions of relevance to enzyme catalysis: Trypsin, catechol O-methyltransferase, β-lactamase and pseudouridine synthase Journal of the Chemical Society. Perkin Transactions 2. 409-415. DOI: 10.1039/A907793F |
0.567 |
|
| 2000 |
Massova I, Kollman PA. Combined molecular mechanical and continuum solvent approach (MM- PBSA/GBSA) to predict ligand binding Perspectives in Drug Discovery and Design. 18: 113-135. DOI: 10.1023/A:1008763014207 |
0.36 |
|
| 2000 |
Kuhn B, Kollman PA. A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning Journal of the American Chemical Society. 122: 3909-3916. DOI: 10.1021/Ja994180S |
0.394 |
|
| 2000 |
Simmerling C, Lee MR, Ortiz AR, Kolinski A, Skolnick J, Kollman PA. Combining MONSSTER and LES/PME to predict protein structure from amino acid sequence: Application to the small protein CMTI-1 Journal of the American Chemical Society. 122: 8392-8402. DOI: 10.1021/Ja993119K |
0.403 |
|
| 2000 |
Kuhn B, Kollman PA. QM-FE and molecular dynamics calculations on catechol O- methyltransferase: Free energy of activation in the enzyme and in aqueous solution and regioselectivity of the enzyme-catalyzed reaction Journal of the American Chemical Society. 122: 2586-2596. DOI: 10.1021/Ja992218V |
0.397 |
|
| 2000 |
Peräkylä M, Kollman PA. Why does trypsin cleave BPTI so slowly? Journal of the American Chemical Society. 122: 3436-3444. DOI: 10.1021/Ja991602P |
0.342 |
|
| 2000 |
Donini O, Darden T, Kollman PA. QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: Reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed Journal of the American Chemical Society. 122: 12270-12280. DOI: 10.1021/Ja001043I |
0.343 |
|
| 2000 |
Kollman P. Molecular dynamics simulations on protein folding and protein structure prediction Journal of Molecular Graphics & Modelling. 18: 553. DOI: 10.1016/S1093-3263(00)80122-9 |
0.344 |
|
| 2000 |
Wang J, Cieplak P, Kollman PA. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? Journal of Computational Chemistry. 21: 1049-1074. DOI: 10.1002/1096-987X(200009)21:12<1049::Aid-Jcc3>3.0.Co;2-F |
0.376 |
|
| 2000 |
Grabuleda X, Jaime C, Kollman PA. Molecular Dynamics Simulation Studies of Liquid Acetonitrile: New Six-Site Model Journal of Computational Chemistry. 21: 901-908. DOI: 10.1002/1096-987X(20000730)21:10<901::Aid-Jcc7>3.0.Co;2-F |
0.371 |
|
| 1999 |
Chong LT, Duan Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proceedings of the National Academy of Sciences of the United States of America. 96: 14330-5. PMID 10588705 DOI: 10.1073/Pnas.96.25.14330 |
0.672 |
|
| 1999 |
Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proceedings of the National Academy of Sciences of the United States of America. 96: 9997-10002. PMID 10468550 DOI: 10.1073/Pnas.96.18.9997 |
0.568 |
|
| 1999 |
Dixon RW, Kollman P. The free energies for mutating S27 and W79 to alanine in streptavidin and its biotin complex: The relative size of polar and nonpolar free energies on biotin binding Proteins: Structure, Function and Genetics. 36: 471-473. PMID 10450089 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<471::Aid-Prot11>3.0.Co;2-6 |
0.372 |
|
| 1999 |
Pitera JW, Munagala NR, Wang CC, Kollman PA. Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment. Biochemistry. 38: 10298-306. PMID 10441123 DOI: 10.1021/Bi990250W |
0.669 |
|
| 1999 |
Wang L, Duan Y, Shortle R, Imperiali B, Kollman PA. Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Science : a Publication of the Protein Society. 8: 1292-304. PMID 10386879 DOI: 10.1110/Ps.8.6.1292 |
0.353 |
|
| 1999 |
Wang J, Kollman PA, Kuntz ID. Flexible ligand docking: a multistep strategy approach. Proteins. 36: 1-19. PMID 10373002 DOI: 10.1002/(Sici)1097-0134(19990701)36:1<1::Aid-Prot1>3.0.Co;2-T |
0.618 |
|
| 1999 |
Wang J, Dixon R, Kollman PA. Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study. Proteins. 34: 69-81. PMID 10336384 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<69::Aid-Prot6>3.0.Co;2-C |
0.428 |
|
| 1999 |
Cheatham TE, Cieplak P, Kollman PA. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. Journal of Biomolecular Structure & Dynamics. 16: 845-62. PMID 10217454 DOI: 10.1080/07391102.1999.10508297 |
0.594 |
|
| 1999 |
McCarrick MA, Kollman PA. Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations. Journal of Computer-Aided Molecular Design. 13: 109-21. PMID 10091118 DOI: 10.1023/A:1008044721715 |
0.388 |
|
| 1999 |
Eriksson MA, Pitera J, Kollman PA. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. Journal of Medicinal Chemistry. 42: 868-81. PMID 10072684 DOI: 10.1021/Jm980277Y |
0.7 |
|
| 1999 |
Konerding DE, Cheatham TE, Kollman PA, James TL. Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. Journal of Biomolecular Nmr. 13: 119-31. PMID 10070753 DOI: 10.1023/A:1008353423074 |
0.625 |
|
| 1999 |
Reyes CM, Kollman PA. Molecular dynamics studies of U1A-RNA complexes. Rna (New York, N.Y.). 5: 235-44. PMID 10024175 DOI: 10.1017/S1355838299981657 |
0.596 |
|
| 1999 |
Wang W, Wang J, Kollman PA. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins. 34: 395-402. PMID 10024025 DOI: 10.1002/(Sici)1097-0134(19990215)34:3<395::Aid-Prot11>3.0.Co;2-4 |
0.41 |
|
| 1999 |
Vacek J, Kollman PA. Binding free energy and extraction selectivity calculations of anisole and phenanthroline spherands Journal of Physical Chemistry A. 103: 10015-10020. DOI: 10.1021/Jp993174F |
0.394 |
|
| 1999 |
Peräkylä M, Kollman PA. Ab Initio Quantum Mechanical and Molecular Dynamical Study of Intra- and Intermolecular Anhydride Formation Journal of Physical Chemistry A. 103: 8067-8074. DOI: 10.1021/Jp990619R |
0.401 |
|
| 1999 |
Eriksson MAL, Morgantini PY, Kollman PA. Binding of organic cations to a cyclophane host as studied with molecular dynamics simulations and free energy calculations Journal of Physical Chemistry B. 103: 4474-4480. DOI: 10.1021/Jp983513P |
0.439 |
|
| 1999 |
Cho SJ, Kollman PA. Free energy perturbation and molecular dynamics studies of [16]starand with various alkali metal ions Journal of Organic Chemistry. 64: 5787-5793. DOI: 10.1021/Jo982367G |
0.341 |
|
| 1999 |
Lee TS, Kollman PA. Quantum mechanical calculations of nucleophilic attack in the pseudouridine synthesis reaction Journal of the American Chemical Society. 121: 9928-9931. DOI: 10.1021/Ja991088N |
0.312 |
|
| 1999 |
Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies Journal of the American Chemical Society. 121: X. DOI: 10.1021/Ja990935J |
0.4 |
|
| 1999 |
Bakowies D, Kollman PA. Theoretical study of base-catalyzed amide hydrolysis: Gas- and aqueous-phase hydrolysis of formamide Journal of the American Chemical Society. 121: 5712-5726. DOI: 10.1021/Ja9837349 |
0.321 |
|
| 1999 |
Singh SB, Kollman PA. Calculating the absolute free energy of association of netropsin and DNA Journal of the American Chemical Society. 121: 3267-3271. DOI: 10.1021/Ja983118C |
0.375 |
|
| 1999 |
Pang YP, Miller JL, Kollman PA. Computational and experimental studies of (2,2)-Bis(indol-1-yl- methyl)acetate suggest the importance of the hydrophobic effect in aromatic stacking interactions Journal of the American Chemical Society. 121: 1717-1725. DOI: 10.1021/Ja9828410 |
0.4 |
|
| 1999 |
Garcia-Viloca M, Kollman PA. Molecular Dynamics Simulations Can Reproduce the Subtle Differences in NADP and NHDP Binding to Isocitrate Dehydrogenase International Journal of Quantum Chemistry. 75: 231-243. DOI: 10.1002/(Sici)1097-461X(1999)75:3<231::Aid-Qua13>3.0.Co;2-A |
0.363 |
|
| 1998 |
Srinivasan J, Miller J, Kollman PA, Case DA. Continuum solvent studies of the stability of RNA hairpin loops and helices. Journal of Biomolecular Structure & Dynamics. 16: 671-82. PMID 10052623 DOI: 10.1080/07391102.1998.10508279 |
0.439 |
|
| 1998 |
Cheatham TE, Srinivasan J, Case DA, Kollman PA. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. Journal of Biomolecular Structure & Dynamics. 16: 265-80. PMID 9833666 DOI: 10.1080/07391102.1998.10508245 |
0.654 |
|
| 1998 |
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (New York, N.Y.). 282: 740-4. PMID 9784131 DOI: 10.1126/Science.282.5389.740 |
0.376 |
|
| 1998 |
Radmer RJ, Kollman PA. The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. Journal of Computer-Aided Molecular Design. 12: 215-27. PMID 9749366 DOI: 10.1023/A:1007905722422 |
0.403 |
|
| 1998 |
Wang L, Veenstra DL, Radmer RJ, Kollman PA. Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods. Proteins. 32: 438-58. PMID 9726415 DOI: 10.1002/(Sici)1097-0134(19980901)32:4<438::Aid-Prot4>3.0.Co;2-C |
0.348 |
|
| 1998 |
Duan Y, Wang L, Kollman PA. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. 95: 9897-902. PMID 9707572 DOI: 10.1073/Pnas.95.17.9897 |
0.384 |
|
| 1998 |
Pitera J, Kollman P. Graphical visualization of mean hydration from molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 15: 355-8, 386-8. PMID 9704297 DOI: 10.1016/S1093-3263(98)00006-0 |
0.677 |
|
| 1998 |
Kollman P. Recent Advances in Structure-Based Ligand Design Using Molecular Dynamics and Monte Carlo Methods Pharmaceutical Research. 15: 368-370. PMID 9563064 DOI: 10.1023/A:1011903711265 |
0.35 |
|
| 1998 |
Spector TI, Kollman PA. Investigation of the anomalous solvation free energies of amides and amines: FEP calculations in cyclohexane and PS-GVB calculations on amide-water complexes Journal of Physical Chemistry B. 102: 4004-4010. DOI: 10.1021/Jp972593E |
0.396 |
|
| 1998 |
Fox T, Kollman PA. Application of the RESP methodology in the parametrization of organic solvents Journal of Physical Chemistry B. 102: 8070-8079. DOI: 10.1021/Jp9717655 |
0.302 |
|
| 1998 |
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices Journal of the American Chemical Society. 120: 9401-9409. DOI: 10.1021/Ja981844+ |
0.626 |
|
| 1998 |
Wang J, Kollman PA. Alkali cation extraction by 18-crown-6 and its derivatives: A free energy perturbation study Journal of the American Chemical Society. 120: 11106-11114. DOI: 10.1021/Ja980464L |
0.371 |
|
| 1998 |
Pitera J, Kollman P. Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball” Journal of the American Chemical Society. 120: 7557-7567. DOI: 10.1021/Ja973028S |
0.669 |
|
| 1998 |
Stanton RV, Peräkylä M, Bakowies D, Kollman PA. Combined ab initio and free energy calculations to study reactions in enzymes and solution: Amide hydrolysis in trypsin and aqueous solution Journal of the American Chemical Society. 120: 3448-3457. DOI: 10.1021/Ja972723X |
0.349 |
|
| 1998 |
Simmerling C, Miller JL, Kollman PA. Combined locally enhanced sampling and Particle Mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid Journal of the American Chemical Society. 120: 7149-7155. DOI: 10.1021/Ja9727023 |
0.304 |
|
| 1998 |
Simmerling C, Fox T, Kollman PA. Use of locally enhanced sampling in free energy calculations: Testing and application to the α → β anomerization of glucose Journal of the American Chemical Society. 120: 5771-5782. DOI: 10.1021/Ja972457N |
0.316 |
|
| 1998 |
Kollman P, Weinstein H, Zerner M. Introduction: Theoretical chemistry in biology: From molecular structure to functional mechanisms International Journal of Quantum Chemistry. 69: 1-1. DOI: 10.1002/(Sici)1097-461X(1998)69:1<1::Aid-Qua1>3.0.Co;2-Z |
0.326 |
|
| 1998 |
Cheatham TE, Miller JL, Spector TI, Cieplak P, Kollman PA. Molecular Dynamics Simulations on Nucleic Acid Systems Using the Cornell et al. Force Field and Particle Mesh Ewald Electrostatics Acs Symposium Series. 682: 285-303. |
0.533 |
|
| 1997 |
Miller JL, Kollman PA. Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics. Biophysical Journal. 73: 2702-10. PMID 9370463 DOI: 10.1016/S0006-3495(97)78298-5 |
0.361 |
|
| 1997 |
Cheatham TE, Kollman PA. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). Structure (London, England : 1993). 5: 1297-311. PMID 9351805 DOI: 10.1016/S0969-2126(97)00282-7 |
0.59 |
|
| 1997 |
Veenstra DL, Kollman PA. Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants. Protein Engineering. 10: 789-807. PMID 9342145 DOI: 10.1093/Protein/10.7.789 |
0.377 |
|
| 1997 |
Cheatham TE, Crowley MF, Fox T, Kollman PA. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proceedings of the National Academy of Sciences of the United States of America. 94: 9626-30. PMID 9275173 DOI: 10.1073/Pnas.94.18.9626 |
0.526 |
|
| 1997 |
Miller JL, Kollman PA. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. Journal of Molecular Biology. 270: 436-50. PMID 9237909 DOI: 10.1006/Jmbi.1997.1113 |
0.37 |
|
| 1997 |
Eksterowicz JE, Miller JL, Kollman PA. Calculation of chloroform/water partition coefficients for the N-methylated nucleic acid bases Journal of Physical Chemistry B. 101: 10971-10975. DOI: 10.1021/Jp972440R |
0.369 |
|
| 1997 |
Spector TI, Cheatham TE, Kollman PA. Unrestrained molecular dynamics of photodamaged DNA in aqueous solution Journal of the American Chemical Society. 119: 7095-7104. DOI: 10.1021/Ja964372C |
0.606 |
|
| 1997 |
Fox T, Scanlan TS, Kollman PA. Ligand binding in the catalytic antibody 17E8. A free energy perturbation calculation study Journal of the American Chemical Society. 119: 11571-11577. DOI: 10.1021/Ja964315J |
0.369 |
|
| 1997 |
Cieplak P, Cheatham TE, Kollman PA. Molecular dynamics simulations find that 3' phosphoramidate modified DNA duplexes undergo a B to A transition and normal DNA duplexes an A to B transition Journal of the American Chemical Society. 119: 6722-6730. DOI: 10.1021/Ja963909J |
0.592 |
|
| 1997 |
Cheatham TE, Kollman PA. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes Journal of the American Chemical Society. 119: 4805-4825. DOI: 10.1021/Ja963641W |
0.572 |
|
| 1997 |
Peräkylä M, Kollman PA. A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics Journal of the American Chemical Society. 119: 1189-1196. DOI: 10.1021/Ja9628967 |
0.395 |
|
| 1997 |
Cornell WD, Gould IR, Kollman PA. The effects of basis set and blocking groups on the conformational energies of glycyl and alanyl dipeptides A Hartree-Fock and MP2 study Journal of Molecular Structure: Theochem. 392: 101-109. DOI: 10.1016/S0166-1280(97)90383-3 |
0.724 |
|
| 1997 |
Dixon RW, Kollman PA. Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics Journal of Computational Chemistry. 18: 1632-1646. DOI: 10.1002/(Sici)1096-987X(199710)18:13<1632::Aid-Jcc5>3.0.Co;2-S |
0.395 |
|
| 1997 |
Radmer RJ, Kollman PA. Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes Journal of Computational Chemistry. 18: 902-919. DOI: 10.1002/(Sici)1096-987X(199705)18:7<902::Aid-Jcc4>3.0.Co;2-V |
0.349 |
|
| 1996 |
Cieplak P, Howard AE, Powers JP, Rychnovsky SD, Kollman PA. Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study. The Journal of Organic Chemistry. 61: 3662-3668. PMID 11667213 DOI: 10.1021/Jo951918P |
0.413 |
|
| 1996 |
Cieplak P, Kollman PA. A technique to study molecular recognition in drug design: preliminary application of free energy derivatives to inhibition of a malarial cysteine protease. Journal of Molecular Recognition : Jmr. 9: 103-12. PMID 8877800 DOI: 10.1002/(Sici)1099-1352(199603)9:2<103::Aid-Jmr246>3.0.Co;2-A |
0.405 |
|
| 1996 |
Fox T, Kollman PA. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"? Proteins. 25: 315-34. PMID 8844867 DOI: 10.1002/(Sici)1097-0134(199607)25:3<315::Aid-Prot4>3.0.Co;2-E |
0.392 |
|
| 1996 |
Sun YC, Veenstra DL, Kollman PA. Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability. Protein Engineering. 9: 273-81. PMID 8736494 DOI: 10.1093/Protein/9.3.273 |
0.433 |
|
| 1996 |
Cheatham TE, Kollman PA. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. Journal of Molecular Biology. 259: 434-44. PMID 8676379 DOI: 10.1006/Jmbi.1996.0330 |
0.604 |
|
| 1996 |
Miller JL, Kollman PA. Solvation free energies of the nucleic acid bases Journal of Physical Chemistry. 100: 8587-8594. DOI: 10.1021/Jp9605358 |
0.396 |
|
| 1996 |
Fox T, Thomas BE, McCarrick aM, Kollman PA. Application of Free Energy Perturbation Calculations to the “Tennis Ball” Dimer: Why Is CF4 Not Encapsulated by This Host? The Journal of Physical Chemistry. 100: 10779-10783. DOI: 10.1021/Jp960256K |
0.322 |
|
| 1996 |
Meng EC, Kollman PA. Molecular dynamics studies of the properties of water around simple organic solutes Journal of Physical Chemistry. 100: 11460-11470. DOI: 10.1021/Jp9536209 |
0.352 |
|
| 1996 |
Meng EC, Caldwell JW, Kollman PA. Investigating the anomalous solvation free energies of amines with a polarizable potential Journal of Physical Chemistry. 100: 2367-2371. DOI: 10.1021/Jp952463A |
0.399 |
|
| 1996 |
Fox T, Kollman PA. Calculation of ionization potentials and C-H bond dissociation energies of toluene derivatives Journal of Physical Chemistry. 100: 2950-2956. DOI: 10.1021/Jp952046Y |
0.376 |
|
| 1996 |
Sun Y, Kollman P. Are There Water-Bridge-Induced Hydrophilic Interactions? The Journal of Physical Chemistry. 100: 6760-6763. DOI: 10.1021/Jp950840D |
0.635 |
|
| 1996 |
Nowakowski J, Miller JL, Kollman PA, Tinoco I. Time evolution of NMR proton chemical shifts of an RNA hairpin during a molecular dynamics simulation Journal of the American Chemical Society. 118: 12812-12820. DOI: 10.1021/Ja9625945 |
0.369 |
|
| 1996 |
Chipot C, Jaffe R, Maigret B, Pearlman DA, Kollman PA. Benzene dimer: A good model for π-π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution Journal of the American Chemical Society. 118: 11217-11224. DOI: 10.1021/Ja961379L |
0.362 |
|
| 1996 |
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesJ.Am.Chem.Soc.1995,117, 5179−5197 Journal of the American Chemical Society. 118: 2309-2309. DOI: 10.1021/Ja955032E |
0.683 |
|
| 1996 |
Chipot C, Maigret B, Pearlman DA, Kollman PA. Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene−Ammonium π-Cation Interactions Journal of the American Chemical Society. 118: 2998-3005. DOI: 10.1021/Ja950302E |
0.406 |
|
| 1996 |
Kollman PA. Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules Accounts of Chemical Research. 29: X-469. DOI: 10.1021/Ar9500675 |
0.4 |
|
| 1996 |
Alagona G, Ghio C, Kollman PA. Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: Isomerization catalyzed by triose phosphate isomerase (TIM) Journal of Molecular Structure: Theochem. 371: 287-298. DOI: 10.1016/S0166-1280(96)04667-2 |
0.34 |
|
| 1996 |
Cornell WD, Ha MP, Sun Y, Kollman PA. Application of a simple diagonal force Field to the simulation of cyclopentane conformational dynamics Journal of Computational Chemistry. 17: 1541-1548. DOI: 10.1002/(Sici)1096-987X(199610)17:13<1541::Aid-Jcc5>3.0.Co;2-S |
0.736 |
|
| 1996 |
Chipot C, Kollman PA, Pearlman DA. Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions Journal of Computational Chemistry. 17: 1112-1131. DOI: 10.1002/(Sici)1096-987X(19960715)17:9<1112::Aid-Jcc4>3.0.Co;2-V |
0.428 |
|
| 1995 |
Rastelli G, Thomas B, Kollman PA, Santi DV. Insight into the specificity of thymidylate synthase from molecular dynamics and free energy perturbation calculations Journal of the American Chemical Society. 117: 7213-7227. DOI: 10.1021/Ja00132A022 |
0.426 |
|
| 1995 |
Morgantini PY, Kollman PA. Solvation free energies of amides and amines: Disagreement between free energy calculations and experiment Journal of the American Chemical Society. 117: 6057-6063. DOI: 10.1021/Ja00127A019 |
0.392 |
|
| 1995 |
DeBolt SE, Kollman PA. Investigation of structure, dynamics, and solvation in 1-octanol and its water-saturated solution: Molecular dynamics and free-energy perturbation studies Journal of the American Chemical Society. 117: 5316-5340. DOI: 10.1021/Ja00124A015 |
0.382 |
|
| 1995 |
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules Journal of the American Chemical Society. 117: 5179-5197. DOI: 10.1021/Ja00124A002 |
0.743 |
|
| 1995 |
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins Journal of the American Chemical Society. 117: 4193-4194. DOI: 10.1021/Ja00119A045 |
0.589 |
|
| 1995 |
Sun Y, Kollman PA. Quantitation and nature of the macrocyclic effect: K+ complexation with 18-crown-6 and pentaglyme Journal of the American Chemical Society. 117: 3599-3604. DOI: 10.1021/Ja00117A028 |
0.519 |
|
| 1995 |
Sun Y, Caldwell JW, Kollman PA. Molecular dynamics and free energy perturbation study of spherand complexation with metal ions employing additive and nonadditive force fields Journal of Physical Chemistry. 99: 10081-10085. DOI: 10.1021/J100025A006 |
0.607 |
|
| 1995 |
Dang LX, Kollman PA. Free Energy of Association of the K+:18-Crown-6 Complex in Water: A New Molecular Dynamics Study The Journal of Physical Chemistry. 99: 55-58. DOI: 10.1021/J100001A011 |
0.402 |
|
| 1995 |
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules Computer Physics Communications. 91: 1-41. DOI: 10.1016/0010-4655(95)00041-D |
0.619 |
|
| 1995 |
Pang YP, Kollman PA. Applications of free energy derivatives to analog design Perspectives in Drug Discovery and Design. 3: 106-122. DOI: 10.1007/Bf02174469 |
0.365 |
|
| 1995 |
-Amant AS, Cornell WD, Kollman PA, Halgren TA. Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory Journal of Computational Chemistry. 16: 1483-1506. DOI: 10.1002/Jcc.540161206 |
0.716 |
|
| 1995 |
Cieplak P, Cornell WD, Bayly CI, Kollman PA. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins Journal of Computational Chemistry. 16: 1357-1377. DOI: 10.1002/Jcc.540161106 |
0.666 |
|
| 1995 |
Duan Y, Kumar S, Rosenberg JM, Kollman PA. Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations Journal of Computational Chemistry. 16: 1351-1356. DOI: 10.1002/Jcc.540161105 |
0.38 |
|
| 1995 |
Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA. Multidimensional free-energy calculations using the weighted histogram analysis method Journal of Computational Chemistry. 16: 1339-1350. DOI: 10.1002/Jcc.540161104 |
0.36 |
|
| 1995 |
Sun Y, Kollman PA. Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model Journal of Computational Chemistry. 16: 1164-1169. DOI: 10.1002/Jcc.540160910 |
0.619 |
|
| 1995 |
Howard AE, Cieplak P, Kollman PA. A molecular mechanical model that reproduces the relative energies for chair and twist‐boat conformations of 1,3‐dioxanes Journal of Computational Chemistry. 16: 243-261. DOI: 10.1002/Jcc.540160211 |
0.442 |
|
| 1994 |
Guenot J, Fletterick RJ, Kollman PA. A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA. Protein Science : a Publication of the Protein Society. 3: 1276-85. PMID 7987223 DOI: 10.1002/Pro.5560030814 |
0.314 |
|
| 1994 |
McCarrick MA, Kollman P. [20] Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design Methods in Enzymology. 241: 370-384. PMID 7854189 DOI: 10.1016/0076-6879(94)41074-7 |
0.385 |
|
| 1994 |
Grootenhuis PD, Roe DC, Kollman PA, Kuntz ID. Finding potential DNA-binding compounds by using molecular shape. Journal of Computer-Aided Molecular Design. 8: 731-50. PMID 7738607 DOI: 10.1007/Bf00124018 |
0.537 |
|
| 1994 |
Kumar S, Duan Y, Kollman PA, Rosenberg JM. Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. Journal of Biomolecular Structure & Dynamics. 12: 487-525. PMID 7727057 DOI: 10.1080/07391102.1994.10508757 |
0.411 |
|
| 1994 |
Chipot C, Millot C, Maigret B, Kollman PA. Molecular dynamics free energy simulations: Influence of the truncation of long-range nonbonded electrostatic interactions on free energy calculations of polar molecules The Journal of Chemical Physics. 101: 7953-7962. DOI: 10.1063/1.468222 |
0.433 |
|
| 1994 |
Cieplak P, Pearlman DA, Kollman PA. Walking on the free energy hypersurface of the 18-crown-6 ion system using free energy derivatives The Journal of Chemical Physics. 101: 627-633. DOI: 10.1063/1.468117 |
0.395 |
|
| 1994 |
Meng EC, Cieplak P, Caldwell JW, Kollman PA. Accurate solvation free energies of acetate and methylammonium ions calculated with a polarizable water model Journal of the American Chemical Society. 116: 12061-12062. DOI: 10.1021/Ja00105A060 |
0.358 |
|
| 1994 |
Thomas BE, Kollman PA. Free energy perturbation calculations of the relative binding affinities of an 8-subunit cavitand for alkali ions in methanol Journal of the American Chemical Society. 116: 3449-3452. DOI: 10.1021/Ja00087A034 |
0.356 |
|
| 1994 |
Bayly CI, Kollman PA. Molecular dynamics and free energy calculations on the peculiar bimodal alkali ion selectivity of an 8-subunit cavitand Journal of the American Chemical Society. 116: 697-703. DOI: 10.1021/Ja00081A034 |
0.418 |
|
| 1994 |
Chipot C, Millot C, Maigret B, Kollman PA. Molecular dynamics free energy perturbation calculations: Influence of nonbonded parameters on the free energy of hydration of charged and neutral species Journal of Physical Chemistry. 98: 11362-11372. DOI: 10.1021/J100095A019 |
0.398 |
|
| 1994 |
Kollman PA. Theory of macromolecule-ligand interactions Current Opinion in Structural Biology. 4: 240-245. DOI: 10.1016/S0959-440X(94)90315-8 |
0.358 |
|
| 1994 |
DeBolt SE, Pearlman DA, Kollman PA. Free energy perturbation calculations on parallel computers: demonstrations of scalable linear speedup Journal of Computational Chemistry. 15: 351-373. DOI: 10.1002/Jcc.540150310 |
0.417 |
|
| 1993 |
Yamaotsu N, Moriguchi I, Kollman PA, Hirono S. Molecular dynamics study of the stability of staphylococcal nuclease mutants: component analysis of the free energy difference of denaturation. Biochimica Et Biophysica Acta. 1163: 81-8. PMID 8476933 DOI: 10.1016/0167-4838(93)90282-V |
0.414 |
|
| 1993 |
Miyamoto S, Kollman PA. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proceedings of the National Academy of Sciences of the United States of America. 90: 8402-6. PMID 8378312 DOI: 10.1073/Pnas.90.18.8402 |
0.405 |
|
| 1993 |
Cieplak P, Kollman PA. Peptide mimetics as enzyme inhibitors: use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor. Journal of Computer-Aided Molecular Design. 7: 291-304. PMID 8377026 DOI: 10.1007/Bf00125504 |
0.348 |
|
| 1993 |
Miyamoto S, Kollman PA. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins. 16: 226-45. PMID 8346190 DOI: 10.1002/Prot.340160303 |
0.472 |
|
| 1993 |
Singh SB, Pearlman DA, Kollman PA. Free energy component analysis: application to the "Z-phobicity" of A-T base pairs. Journal of Biomolecular Structure & Dynamics. 11: 303-11. PMID 8286058 DOI: 10.1080/07391102.1993.10508728 |
0.335 |
|
| 1993 |
Lopez MA, Kollman PA. Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems II: CO and dioxygen binding to myoglobin. Protein Science : a Publication of the Protein Society. 2: 1975-86. PMID 8268807 DOI: 10.1002/Pro.5560021119 |
0.391 |
|
| 1993 |
Rao SN, Kollman PA. Theoretical Simulations on d(CGCGAATTCGCG)2 with cis-syn Thymine–Thymine Cyclobutane Dimer Bulletin of the Chemical Society of Japan. 66: 3132-3134. DOI: 10.1246/Bcsj.66.3132 |
0.38 |
|
| 1993 |
Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field Molecular Simulation. 10: 121-149. DOI: 10.1080/08927029308022162 |
0.371 |
|
| 1993 |
Gough CA, Pearlman DA, Kollman P. Calculations of the relative free energies of aqueous solvation of several fluorocarbons: A test of the bond potential of mean force correction Journal of Chemical Physics. 99: 9103-9110. DOI: 10.1063/1.465525 |
0.417 |
|
| 1993 |
Cornell WD, Cieplak P, Bayly CI, Kollman PA. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation Journal of the American Chemical Society. 115: 9620-9631. DOI: 10.1021/Ja00074A030 |
0.726 |
|
| 1993 |
Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model Journal of Physical Chemistry. 97: 10269-10280. DOI: 10.1021/J100142A004 |
0.695 |
|
| 1993 |
Kollman P. Free Energy Calculations : Applications To Chemical And Biochemical Phenomena Chemical Reviews. 93: 2395-2417. DOI: 10.1021/Cr00023A004 |
0.426 |
|
| 1993 |
DeBolt SE, Kollman PA. AMBERCUBE MD, parallelization of AMBER's molecular dynamics module for distributed-memory hypercube computers Journal of Computational Chemistry. 14: 312-329. DOI: 10.1002/Jcc.540140307 |
0.32 |
|
| 1993 |
Guenot J, Kollman PA. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation Journal of Computational Chemistry. 14: 295-311. DOI: 10.1002/Jcc.540140306 |
0.388 |
|
| 1992 |
Mendel D, Ellman JA, Chang Z, Veenstra DL, Kollman PA, Schultz PG. Probing protein stability with unnatural amino acids. Science (New York, N.Y.). 256: 1798-802. PMID 1615324 DOI: 10.1126/Science.1615324 |
0.317 |
|
| 1992 |
Banci L, Schröder S, Kollman PA. Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts. Proteins. 13: 288-305. PMID 1518800 DOI: 10.1002/Prot.340130403 |
0.401 |
|
| 1992 |
Dahl SG, Kollman PA, Rao SN, Singh UC. Structural changes by sulfoxidation of phenothiazine drugs. Journal of Computer-Aided Molecular Design. 6: 207-22. PMID 1355521 DOI: 10.1007/Bf00123377 |
0.347 |
|
| 1992 |
Guenot J, Kollman PA. Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. Protein Science : a Publication of the Protein Society. 1: 1185-205. PMID 1304396 DOI: 10.1002/Pro.5560010912 |
0.381 |
|
| 1992 |
Howard AE, Kollman PA. Molecular dynamics studies of a DNA-binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations. Protein Science : a Publication of the Protein Society. 1: 1173-84. PMID 1304395 DOI: 10.1002/Pro.5560010911 |
0.385 |
|
| 1992 |
Schiffer CA, Caldwell JW, Stroud RM, Kollman PA. Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case. Protein Science : a Publication of the Protein Society. 1: 396-400. PMID 1304346 DOI: 10.1002/Pro.5560010311 |
0.421 |
|
| 1992 |
Hurle MR, Eads CD, Pearlman DA, Seibel GL, Thomason J, Kosen PA, Kollman P, Anderson S, Kuntz ID. Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two-dimensional nuclear magnetic resonance. Protein Science : a Publication of the Protein Society. 1: 91-106. PMID 1284804 DOI: 10.1002/Pro.5560010110 |
0.548 |
|
| 1992 |
Sun Y, Kollman PA. Determination of solvation free energy using molecular dynamics with solute Cartesian mapping: An application to the solvation of 18-crown-6 The Journal of Chemical Physics. 97: 5108-5112. DOI: 10.1063/1.463832 |
0.653 |
|
| 1992 |
Brown FK, Singh UC, Kollman PA, Raimondi L, Houk KN, Bock CW. A theoretical study of intramolecular Diels-Alder and 1,3-dipolar cycloaddition stereoselectivity using ab initio methods, semiempirical methods, and a tandem quantum mechanic-molecular mechanic method Journal of Organic Chemistry. 57: 4862-4869. DOI: 10.1021/Jo00044A021 |
0.324 |
|
| 1992 |
Sun Y, Spellmeyer D, Pearlman DA, Kollman P. Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides : a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale Journal of the American Chemical Society. 114: 6798-6801. DOI: 10.1021/Ja00043A027 |
0.63 |
|
| 1992 |
Leach AR, Kollman PA. Theoretical investigations of novel nucleic acid bases Journal of the American Chemical Society. 114: 3675-3683. DOI: 10.1021/Ja00036A016 |
0.342 |
|
| 1992 |
Miyamoto S, Kollman PA. Molecular dynamics studies of calixspherand complexes with alkali metal cations: Calculation of the absolute and relative free energies of binding of cations to a calixspherand Journal of the American Chemical Society. 114: 3668-3674. DOI: 10.1021/Ja00036A015 |
0.385 |
|
| 1992 |
Gould IR, Kollman PA. Ab initio SCF and MP2 calculations on four low-energy conformers of N-acetyl-N′-methylalaninamide Journal of Physical Chemistry. 96: 9255-9258. DOI: 10.1021/J100202A035 |
0.353 |
|
| 1992 |
Caldwell JW, Kollman PA. Ab initio calculations on aquated chloride (Cl-(H2O)14) clusters: comparison with the results from molecular dynamics simulations The Journal of Physical Chemistry. 96: 8249-8251. DOI: 10.1021/J100200A010 |
0.373 |
|
| 1992 |
Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method Journal of Computational Chemistry. 13: 1011-1021. DOI: 10.1002/Jcc.540130812 |
0.374 |
|
| 1992 |
Veenstra DL, Ferguson DM, Kollman PA. How transferable are hydrogen parameters in molecular mechanics calculations? Journal of Computational Chemistry. 13: 971-978. DOI: 10.1002/Jcc.540130807 |
0.336 |
|
| 1992 |
Ferguson DM, Gould IR, Glauser WA, Schroeder S, Kollman PA. Comparison ofab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems Journal of Computational Chemistry. 13: 525-532. DOI: 10.1002/Jcc.540130413 |
0.431 |
|
| 1992 |
Ferguson DM, Pearlman DA, Swope WC, Kollman PA. Free energy perturbation calculations involving potential function changes Journal of Computational Chemistry. 13: 362-370. DOI: 10.1002/Jcc.540130309 |
0.684 |
|
| 1992 |
Sun Y, Kollman PA. Conformational sampling and ensemble generation by molecular dynamics simulations: 18-Crown-6 as a test case Journal of Computational Chemistry. 13: 33-40. DOI: 10.1002/Jcc.540130105 |
0.63 |
|
| 1991 |
Caldwell JW, Agard DA, Kollman PA. Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket. Proteins. 10: 140-8. PMID 1896427 DOI: 10.1002/Prot.340100207 |
0.4 |
|
| 1991 |
Daggett V, Kollman PA, Kuntz ID. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers. 31: 285-304. PMID 1868159 DOI: 10.1002/Bip.360310304 |
0.671 |
|
| 1991 |
Pearlman DA, Kollman PA. Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. Journal of Molecular Biology. 220: 457-79. PMID 1856868 DOI: 10.1016/0022-2836(91)90024-Z |
0.361 |
|
| 1991 |
Ferguson DM, Kollman PA. Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates. Antisense Research and Development. 1: 243-54. PMID 1821645 DOI: 10.1089/Ard.1991.1.243 |
0.375 |
|
| 1991 |
Kollman PA, Daggett V, Dang LX. The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme. Ciba Foundation Symposium. 161: 91-103; discussion 1. PMID 1814699 |
0.524 |
|
| 1991 |
Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 31: 1115-34. PMID 1786342 DOI: 10.1002/Bip.360310911 |
0.68 |
|
| 1991 |
Hirono S, Kollman PA. Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches. Protein Engineering. 4: 233-43. PMID 1649996 DOI: 10.1093/Protein/4.3.233 |
0.466 |
|
| 1991 |
Pearlman DA, Kollman PA. The overlooked bond-stretching contribution in free energy perturbation calculations The Journal of Chemical Physics. 94: 4532-4545. DOI: 10.1063/1.460608 |
0.422 |
|
| 1991 |
Daggett V, Schroeder S, Kollman P. Catalytic pathway of serine proteases: classical and quantum mechanical calculations Journal of the American Chemical Society. 113: 8926-8935. DOI: 10.1021/Ja00023A047 |
0.515 |
|
| 1991 |
Schroeder S, Daggett V, Kollman P. A comparison of the AM1 and PM3 semiempirical models for evaluating model compounds relevant to catalysis by serine proteases Journal of the American Chemical Society. 113: 8922-8925. DOI: 10.1021/Ja00023A046 |
0.488 |
|
| 1991 |
Pearlman DA, Kollman PA. Evaluating the assumptions underlying force field development and application using free energy conformational maps for nucleosides Journal of the American Chemical Society. 113: 7167-7177. DOI: 10.1021/Ja00019A012 |
0.334 |
|
| 1991 |
Dang LX, Rice JE, Caldwell J, Kollman PA. Ion solvation in polarizable water: Molecular dynamics simulations Journal of the American Chemical Society. 113: 2481-2486. DOI: 10.1021/Ja00007A021 |
0.326 |
|
| 1991 |
Kuyper LF, Hunter RN, Ashton D, Merz KM, Kollman PA. Free energy calculations on the relative solvation free energies of benzene, anisole, and 1,2,3-trimethoxybenzene: Theoretical and experimental analysis of aromatic methoxy solvation Journal of Physical Chemistry. 95: 6661-6666. DOI: 10.1021/J100170A052 |
0.391 |
|
| 1991 |
Cornell WD, Howard AE, Kollman P. Molecular mechanical potential functions and their application to study molecular systems: Current Opinion in Structural Biology 1991, 1:201–212 Current Opinion in Structural Biology. 1: 201-212. DOI: 10.1016/0959-440X(91)90062-X |
0.694 |
|
| 1991 |
Cieplak P, Kollman P. On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis‐ and trans‐N‐methyl‐acetamide Journal of Computational Chemistry. 12: 1232-1236. DOI: 10.1002/Jcc.540121010 |
0.405 |
|
| 1991 |
Ferguson DM, Kollman PA. Can the Lennard-Jones 6-12 function replace the 10-12 form in molecular mechanics calculations? Journal of Computational Chemistry. 12: 620-626. DOI: 10.1002/Jcc.540120512 |
0.359 |
|
| 1990 |
Cieplak P, Rao SN, Hélène C, Montenay-Garestier T, Kollman PA. Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine. Journal of Biomolecular Structure & Dynamics. 5: 361-82. PMID 3271480 DOI: 10.1080/07391102.1987.10506400 |
0.336 |
|
| 1990 |
Rao SN, Kollman PA. Conformations of deoxydinucleoside phosphates containing pyrimidine-pyrimidine photodimers. Indian Journal of Biochemistry & Biophysics. 27: 130-5. PMID 2387595 |
0.308 |
|
| 1990 |
Cieplak P, Rao SN, Grootenhuis PD, Kollman PA. Free energy calculation on base specificity of drug--DNA interactions: application to daunomycin and acridine intercalation into DNA. Biopolymers. 29: 717-27. PMID 2383638 DOI: 10.1002/Bip.360290406 |
0.374 |
|
| 1990 |
Pearlman DA, Kollman PA. The calculated free energy effects of 5-methyl cytosine on the B to Z transition in DNA. Biopolymers. 29: 1193-209. PMID 2369632 DOI: 10.1002/Bip.360290810 |
0.398 |
|
| 1990 |
Dang LX, Pearlman DA, Kollman PA. Why do A.T base pairs inhibit Z-DNA formation? Proceedings of the National Academy of Sciences of the United States of America. 87: 4630-4. PMID 2352940 DOI: 10.1073/Pnas.87.12.4630 |
0.396 |
|
| 1990 |
Rao SN, Kollman P. Simulations of the B‐DNA molecular dynamics of d(CGCGAATTCGCG)2 and d(GCGCGCGCGC)2: An analysis of the role of initial geometry and a comparison of united and all‐atom models Biopolymers. 29: 517-532. PMID 2331514 DOI: 10.1002/Bip.360290307 |
0.334 |
|
| 1990 |
Chiche L, Gregoret LM, Cohen FE, Kollman PA. Protein model structure evaluation using the solvation free energy of folding. Proceedings of the National Academy of Sciences of the United States of America. 87: 3240-3. PMID 2326281 DOI: 10.1073/Pnas.87.8.3240 |
0.377 |
|
| 1990 |
Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. Prediction of homologous protein structures based on conformational searches and energetics. Proteins. 8: 30-43. PMID 2217162 DOI: 10.1002/Prot.340080107 |
0.37 |
|
| 1990 |
Daggett V, Kollman PA. Molecular dynamics simulations of active site mutants of triosephosphate isomerase. Protein Engineering. 3: 677-90. PMID 2217142 DOI: 10.1093/Protein/3.8.677 |
0.544 |
|
| 1990 |
Grootenhuis PD, Kollman PA, Seibel GL, DesJarlais RL, Kuntz ID. Computerized selection of potential DNA binding compounds. Anti-Cancer Drug Design. 5: 237-42. PMID 2169249 |
0.461 |
|
| 1990 |
Hirono S, Kollman PA. Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. Journal of Molecular Biology. 212: 197-209. PMID 2157020 DOI: 10.1016/0022-2836(90)90315-D |
0.414 |
|
| 1990 |
Dang LX, Rice JE, Kollman PA. The effect of water models on the interaction of the sodium–chloride ion pair in water: Molecular dynamics simulations Journal of Chemical Physics. 93: 7528-7529. DOI: 10.1063/1.459714 |
0.323 |
|
| 1990 |
Cieplak P, Kollman P. Monte Carlo simulation of aqueous solutions of Li+ and Na+ using many‐body potentials. Coordination numbers, ion solvation enthalpies, and the relative free energy of solvation Journal of Chemical Physics. 92: 6761-6767. DOI: 10.1063/1.458261 |
0.365 |
|
| 1990 |
Cieplak P, Kollman P, Lybrand T. A new water potential including polarization: Application to gas‐phase, liquid, and crystal properties of water The Journal of Chemical Physics. 92: 6755-6760. DOI: 10.1063/1.458260 |
0.337 |
|
| 1990 |
DeBolt SE, Kollman PA. A theoretical examination of solvatochromism and solute-solvent structuring in simple alkyl carbonyl compounds. Simulations using statistical mechanical free energy perturbation methods Journal of the American Chemical Society. 112: 7515-7524. DOI: 10.1021/Ja00177A010 |
0.386 |
|
| 1990 |
Dang LX, Kollman PA. Free energy of association of the 18-crown-6:K+ complex in water: a molecular dynamics simulation Journal of the American Chemical Society. 112: 5716-5720. DOI: 10.1021/Ja00171A006 |
0.369 |
|
| 1990 |
Dang LX, Kollman PA. Molecular dynamics simulations study of the free energy of association of 9-methyladenine and 1-methylthymine bases in water Journal of the American Chemical Society. 112: 503-507. DOI: 10.1021/Ja00158A005 |
0.392 |
|
| 1990 |
Arad D, Langridge R, Kollman PA. A simulation of the sulfur attack in catalytic pathway of papain using molecular mechanics and semiempirical quantum mechanics Journal of the American Chemical Society. 112: 491-502. DOI: 10.1021/Ja00158A004 |
0.301 |
|
| 1990 |
Spellmeyer DC, Grootenhuis PDJ, Miller MD, Kuyper LF, Kollman PA. Theoretical investigations of the rotational barrier in anisole: an ab initio and molecular dynamics study The Journal of Physical Chemistry. 94: 4483-4491. DOI: 10.1021/J100374A026 |
0.352 |
|
| 1990 |
Hansen LM, Kollman PA. Free energy perturbation calculations on models of active sites: applications to adenosine deaminase inhibitors Journal of Computational Chemistry. 11: 994-1002. DOI: 10.1002/Jcc.540110811 |
0.42 |
|
| 1989 |
Rao SN, Lybrand T, Michaud D, Jerina DM, Kollman PA. Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA. Carcinogenesis. 10: 27-38. PMID 2910528 DOI: 10.1093/Carcin/10.1.27 |
0.378 |
|
| 1989 |
Chiche L, Gaboriaud C, Heitz A, Mornon J, Castro B, Kollman PA. Use of restrained molecular dynamics in water to determine three‐dimensional protein structure: Prediction of the three‐dimensional structure of Ecballium elaterium trypsin inhibitor II Proteins. 6: 405-417. PMID 2622910 DOI: 10.1002/Prot.340060407 |
0.378 |
|
| 1989 |
Creighton S, Rudolph B, Lybrand T, Singh UC, Shafer R, Brown S, Kollman P, Case DA, Andrea T. A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex. Journal of Biomolecular Structure & Dynamics. 6: 929-69. PMID 2590510 DOI: 10.1080/07391102.1989.10506524 |
0.373 |
|
| 1989 |
Ross WS, Hardin CC, Tinoco I, Rao SN, Pearlman DA, Kollman PA. Effects of nucleotide bromination on the stabilities of Z-RNA and Z-DNA: a molecular mechanics/thermodynamic perturbation study. Biopolymers. 28: 1939-57. PMID 2480822 DOI: 10.1002/Bip.360281111 |
0.386 |
|
| 1989 |
Pearlman DA, Kollman PA. The lag between the Hamiltonian and the system configuration in free energy perturbation calculations Journal of Chemical Physics. 91: 7831-7839. DOI: 10.1063/1.457251 |
0.387 |
|
| 1989 |
Pearlman DA, Kollman PA. A new method for carrying out free energy perturbation calculations: Dynamically modified windows Journal of Chemical Physics. 90: 2460-2470. DOI: 10.1063/1.455988 |
0.382 |
|
| 1989 |
Dang LX, Merz KM, Kollman PA. Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme Journal of the American Chemical Society. 111: 8505-8508. DOI: 10.1021/Ja00204A027 |
0.33 |
|
| 1989 |
Daggett V, Brown F, Kollman P. Free energy component analysis: a study of the glutamic acid 165 .fwdarw. aspartic acid 165 mutation in triosephosphate isomerase Journal of the American Chemical Society. 111: 8247-8256. DOI: 10.1021/Ja00203A028 |
0.518 |
|
| 1989 |
Lopez MA, Kollman PA. Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. I. Carbon monoxide and dioxygen binding to four heme systems Journal of the American Chemical Society. 111: 6212-6222. DOI: 10.1021/Ja00198A036 |
0.35 |
|
| 1989 |
Merz KM, Kollman PA. Free energy perturbation simulations of the inhibition of thermolysin: prediction of the free energy of binding of a new inhibitor Journal of the American Chemical Society. 111: 5649-5658. DOI: 10.1021/Ja00197A022 |
0.371 |
|
| 1989 |
Grootenhuis PDJ, Kollman PA. Crown ether-neutral molecule interactions studied by molecular mechanics, normal mode analysis, and free energy perturbation calculations. Near quantitative agreement between theory and experimental binding free energies Journal of the American Chemical Society. 111: 4046-4051. DOI: 10.1021/Ja00193A042 |
0.414 |
|
| 1989 |
Gehin D, Kollman PA, Wipff G. Anchoring of ammonium cations to an 18-crown-6 binding site: molecular mechanics and dynamics study Journal of the American Chemical Society. 111: 3011-3023. DOI: 10.1021/Ja00190A040 |
0.332 |
|
| 1989 |
Grootenhuis PDJ, Kollman PA. Molecular mechanics and dynamics studies of crown ether - cation interactions: free energy calculations on the cation selectivity of dibenzo-18-crown-6 and dibenzo-30-crown-10 Journal of the American Chemical Society. 111: 2152-2158. DOI: 10.1021/Ja00188A032 |
0.429 |
|
| 1988 |
Kollman P, van Gunsteren WF. Molecular mechanics and dynamics in protein design. Methods in Enzymology. 154: 430-49. PMID 3481014 DOI: 10.1016/0076-6879(87)54089-7 |
0.372 |
|
| 1988 |
Remers WA, Rao SN, Wunz TP, Kollman PA. Conformations of complexes between mitomycins and decanucleotides. 3. Sequence specificity, binding at C-10, and mitomycin analogs Journal of Medicinal Chemistry. 31: 1612-1620. PMID 3397999 DOI: 10.1021/Jm00403A021 |
0.324 |
|
| 1988 |
Tilton RF, Singh UC, Kuntz ID, Kollman PA. Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. Journal of Molecular Biology. 199: 195-211. PMID 3351919 DOI: 10.1016/0022-2836(88)90389-0 |
0.559 |
|
| 1988 |
Billeter M, Howard AE, Kuntz ID, Kollman PA. A new technique to calculate low-energy conformations of cyclic molecules utilizing the ellipsoid algorithm and molecular dynamics: application to 18-crown-6 Journal of the American Chemical Society. 110: 8385-8391. DOI: 10.1021/Ja00233A016 |
0.384 |
|
| 1988 |
Cieplak P, Kollman PA. Calculation of the free energy of association of nucleic acid bases in vacuo and water solution Journal of the American Chemical Society. 110: 3734-3739. DOI: 10.1021/Ja00220A003 |
0.352 |
|
| 1988 |
Alagona G, Ghio C, Kollman PA. Monte Carlo simulation studies of the solvation of ions. 2. Glycine zwitterion Journal of Molecular Structure-Theochem. 166: 385-392. DOI: 10.1016/0166-1280(88)80466-4 |
0.345 |
|
| 1987 |
Bash PA, Singh UC, Brown FK, Langridge R, Kollman PA. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (New York, N.Y.). 235: 574-6. PMID 3810157 DOI: 10.1126/Science.3810157 |
0.423 |
|
| 1987 |
Behling RW, Rao SN, Kollman P, Kearns DR. Molecular mechanics and dynamics calculations on (dA)10.(dT)10 incorporating distance constraints derived from NMR relaxation measurements. Biochemistry. 26: 4674-81. PMID 3663617 DOI: 10.1021/Bi00389A013 |
0.39 |
|
| 1987 |
Bash PA, Singh UC, Langridge R, Kollman PA. Free energy calculations by computer simulation. Science (New York, N.Y.). 236: 564-8. PMID 3576184 DOI: 10.1126/Science.3576184 |
0.414 |
|
| 1987 |
Pattabiraman N, Rao SN, Scott K, Langridge R, Kollman PA. Molecular mechanical studies on left- and right-handed B-DNA. Biopolymers. 26: 403-14. PMID 3567319 DOI: 10.1002/Bip.360260308 |
0.327 |
|
| 1987 |
Rao SN, Kollman PA. Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle Proceedings of the National Academy of Sciences of the United States of America. 84: 5735-5739. PMID 3475700 DOI: 10.1073/Pnas.84.16.5735 |
0.392 |
|
| 1987 |
Brown FK, Kollman PA. Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. Journal of Molecular Biology. 198: 533-546. PMID 3430618 DOI: 10.1016/0022-2836(87)90298-1 |
0.349 |
|
| 1987 |
Rao SN, Singh UC, Bash PA, Kollman PA. Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin Nature. 328: 551-554. PMID 3302725 DOI: 10.1038/328551A0 |
0.444 |
|
| 1987 |
Cieplak P, Lybrand TP, Kollman PA. Calculation of free energy changes in ion–water clusters using nonadditive potentials and the Monte Carlo method Journal of Chemical Physics. 86: 6393-6403. DOI: 10.1063/1.452428 |
0.356 |
|
| 1987 |
Cieplak P, Bash P, Singh UC, Kollman PA. A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy perturbation methods Journal of the American Chemical Society. 109: 6283-6289. DOI: 10.1021/Ja00255A010 |
0.323 |
|
| 1987 |
Singh UC, Brown FK, Bash PA, Kollman PA. An approach to the application of free energy perturbation methods using molecular dynamics: applications to the transformations of methanol .fwdarw. ethane, oxonium .fwdarw. ammonium, glycine .fwdarw. alanine, and alanine .fwdarw. phenylalanine in aqueous solution and to H3O+(H2O)3 .fwdarw. NH4+(H2O)3 in the gas phase Journal of the American Chemical Society. 109: 1607-1614. DOI: 10.1021/Ja00240A001 |
0.34 |
|
| 1987 |
Cieplak P, Singh UC, Kollman PA. Application of the quantum mechanics and free energy perturbation methods to study molecular processes International Journal of Quantum Chemistry. 32: 65-74. DOI: 10.1002/Qua.560320811 |
0.422 |
|
| 1986 |
Weiner SJ, Kollman PA, Nguyen DT, Case DA. An all atom force field for simulations of proteins and nucleic acids. Journal of Computational Chemistry. 7: 230-252. PMID 29160584 DOI: 10.1002/Jcc.540070216 |
0.368 |
|
| 1986 |
Lybrand TP, Kollman PA, Yu VC, Sadée W. Conformation and electrostatic potential surfaces of opiates: Relationship to µ- and λ-site binding. Pharmaceutical Research. 3: 218-24. PMID 24271585 DOI: 10.1023/A:1016338730077 |
0.303 |
|
| 1986 |
Rao SN, Kollman PA. Hydrogen‐bonding preferences in 2,6‐diaminopurine: uracil (thymine) and 8‐methyl adenine:uracil (thymine) complexes Biopolymers. 25: 267-280. PMID 3955191 DOI: 10.1002/Bip.360250208 |
0.33 |
|
| 1986 |
Tilton RF, Singh UC, Weiner SJ, Connolly ML, Kuntz ID, Kollman PA, Max N, Case DA. Computational studies of the interaction of myoglobin and xenon Journal of Molecular Biology. 192: 443-456. PMID 3560222 DOI: 10.1016/0022-2836(86)90374-8 |
0.608 |
|
| 1986 |
Singh UC, Pattabiraman N, Langridge R, Kollman PA. Molecular mechanical studies of d(CGTACG)2: complex of triostin A with the middle A - T base pairs in either Hoogsteen or Watson-Crick pairing. Proceedings of the National Academy of Sciences of the United States of America. 83: 6402-6. PMID 3462702 DOI: 10.1073/Pnas.83.17.6402 |
0.339 |
|
| 1986 |
Weiner SJ, Seibel GL, Kollman PA. The nature of enzyme catalysis in trypsin. Proceedings of the National Academy of Sciences of the United States of America. 83: 649-653. PMID 3456162 DOI: 10.1073/Pnas.83.3.649 |
0.327 |
|
| 1986 |
Remers WA, Rao SN, Singh UC, Kollman PA. Conformations of complexes between mitomycin and decanucleotides. 2. Application of the model to mitomycin C derivatives. Extension to covalent binding with adenine. Journal of Medicinal Chemistry. 29: 1256-1263. PMID 3100796 DOI: 10.1021/Jm00157A024 |
0.337 |
|
| 1986 |
Kollman PA, Weiner S, Seibel G, Lybrand T, Singh UC, Caldwell J, Rao SN. Modeling complex molecular interactions involving proteins and DNA. Annals of the New York Academy of Sciences. 482: 234-44. PMID 3032040 DOI: 10.1111/J.1749-6632.1986.Tb20954.X |
0.426 |
|
| 1986 |
Alagona G, Ghio C, Kollman PA. Simple model for the effect of Glu165 → Asp165 mutation on the rate of catalysis in triose phosphate isomerase☆ Journal of Molecular Biology. 191: 23-27. PMID 3025454 DOI: 10.1016/0022-2836(86)90419-5 |
0.362 |
|
| 1986 |
Caldwell J, Kollman P. A molecular mechanical study of netropsin-DNA interactions. Biopolymers. 25: 249-266. PMID 3006816 DOI: 10.1002/Bip.360250207 |
0.327 |
|
| 1986 |
Haasnoot CA, Hilbers CW, van der Marel GA, van Boom JH, Singh UC, Pattabiraman N, Kollman PA. On loop folding in nucleic acid hairpin-type structures. Journal of Biomolecular Structure & Dynamics. 3: 843-57. PMID 2482747 DOI: 10.1080/07391102.1986.10508468 |
0.343 |
|
| 1986 |
Singh UC, Kollman PA. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers Journal of Computational Chemistry. 7: 718-730. DOI: 10.1002/Jcc.540070604 |
0.338 |
|
| 1986 |
Rao SN, Singh UC, Kollman PA. Molecular Dynamics Simulations of DNA Double Helices: Studies of Sequence Dependence and the Role of Mismatch Pairs in the DNA Helix Israel Journal of Chemistry. 27: 189-197. DOI: 10.1002/Ijch.198600028 |
0.35 |
|
| 1985 |
Rao SN, Kollman PA. Conformations Of Deoxydodecanucleotides With Pyrimidine (6‐4) Pyrimidone Photoadducts Photochemistry and Photobiology. 42: 465-475. PMID 4089032 DOI: 10.1111/J.1751-1097.1985.Tb01596.X |
0.378 |
|
| 1985 |
Lybrand T, Kollman P. Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA. Biopolymers. 24: 1863-79. PMID 4074844 DOI: 10.1002/Bip.360241003 |
0.385 |
|
| 1985 |
Seibel GL, Singh UC, Kollman PA. A molecular dynamics simulation of double-helical B-DNA including counterions and water Proceedings of the National Academy of Sciences of the United States of America. 82: 6537-6540. PMID 3863112 DOI: 10.1073/Pnas.82.19.6537 |
0.408 |
|
| 1985 |
Lybrand TP, Kollman PA. Water–water and water–ion potential functions including terms for many body effects Journal of Chemical Physics. 83: 2923-2933. DOI: 10.1063/1.449246 |
0.321 |
|
| 1985 |
Singh UC, Kollman PA. A water dimer potential based on ab initio calculations using Morokuma component analyses Journal of Chemical Physics. 83: 4033-4040. DOI: 10.1063/1.449066 |
0.35 |
|
| 1985 |
Kollman P, Wipff G, Singh U. Additions and Corrections - Molecular Mechanical Studies of Inclusion of Alkali Cations into Anisole Spherands Journal of the American Chemical Society. 107: 5025-5025. DOI: 10.1021/Ja00303A601 |
0.336 |
|
| 1985 |
Alagona G, Ghio C, Kollman P. Monte Carlo simulations of the solvation of the dimethyl phosphate anion Journal of the American Chemical Society. 107: 2229-2239. DOI: 10.1021/Ja00294A004 |
0.306 |
|
| 1985 |
Kollman P. Theory of complex molecular interactions: computer graphics, distance geometry, molecular mechanics, and quantum mechanics Accounts of Chemical Research. 18: 105-111. DOI: 10.1021/Ar00112A002 |
0.315 |
|
| 1985 |
Seibel G, Kollman P, Weiner S, Singh UC. Simulation of complex molecules—computational requirements for the 1980's Telematics and Informatics. 2: 307-310. DOI: 10.1016/0736-5853(85)90039-5 |
0.314 |
|
| 1985 |
Singh UC, Kollman P. Energy component analysis calculations on neutral atom …︁ base interactions Journal of Computational Chemistry. 6: 5-8. DOI: 10.1002/Jcc.540060103 |
0.354 |
|
| 1985 |
Kollman PA, Wipff G, Singh UC. Molecular Mechanical Studies Of Inclusion Of Alkali Cations Into Anisole Spherands Cheminform. 16. DOI: 10.1002/Chin.198534089 |
0.327 |
|
| 1985 |
Alagona G, Ghio C, Kollman PA. Monte Carlo Simulations Of The Solvation Of The Dimethyl Phosphate Anion Cheminform. 16. DOI: 10.1002/Chin.198534085 |
0.306 |
|
| 1984 |
Oatley SJ, Blaney JM, Langridge R, Kollman PA. Molecular-mechanical studies of hormone-protein interactions: the interaction of T4 and T3 with prealbumin. Biopolymers. 23: 2931-41. PMID 6525407 DOI: 10.1002/Bip.360231215 |
0.36 |
|
| 1984 |
Keepers JW, Schmidt P, James TL, Kollman PA. Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG) Biopolymers - Peptide Science Section. 23: 2901-2929. PMID 6525406 DOI: 10.1002/Bip.360231214 |
0.357 |
|
| 1984 |
Keepers J, Kollman PA, James TL. Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA Biopolymers - Peptide Science Section. 23: 2499-2511. PMID 6518264 DOI: 10.1002/Bip.360231124 |
0.341 |
|
| 1984 |
Singh UC, Kollman PA. Ab initio calculations on the structure and nature of the hydrogen bonded complex H2S ⋅⋅⋅ HF Journal of Chemical Physics. 80: 353-355. DOI: 10.1063/1.446454 |
0.397 |
|
| 1984 |
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins Journal of the American Chemical Society. 106: 765-784. DOI: 10.1021/Ja00315A051 |
0.459 |
|
| 1984 |
Kollman P. Chapter 2 Non-covalent forces of importance in biochemistry New Comprehensive Biochemistry. 6: 55-71. DOI: 10.1016/S0167-7306(08)60373-7 |
0.323 |
|
| 1984 |
WEINER SJ, KOLLMAN PA, CASE DA, SINGH UC, GHIO C, ALAGONA G, PROFETA SJ, WEINER P. ChemInform Abstract: A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS Chemischer Informationsdienst. 15. DOI: 10.1002/Chin.198419080 |
0.341 |
|
| 1983 |
Tilton RF, Weiner PK, Kollman PA. An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechanics Biopolymers - Peptide Science Section. 22: 969-1002. PMID 6850056 DOI: 10.1002/Bip.360220316 |
0.355 |
|
| 1983 |
Getzoff ED, Tainer JA, Weiner PK, Kollman PA, Richardson JS, Richardson DC. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 306: 287-90. PMID 6646211 DOI: 10.1038/306287A0 |
0.319 |
|
| 1983 |
Weiner PK, Profeta S, Wipff G, Havel T, Kuntz ID, Langridge R, Kollman PA. A distance geometry study of ring systems. Application to cyclooctane, 18-crown-6, cyclododecane and androstanedione Tetrahedron. 39: 1113-1121. DOI: 10.1016/S0040-4020(01)91874-5 |
0.604 |
|
| 1982 |
Brown SC, Kollman PA, Weiner PK. A conformational analysis of daunomycin considering D-ring repucker. Biochimica Et Biophysica Acta. 717: 49-55. PMID 7104390 DOI: 10.1016/0304-4165(82)90378-6 |
0.344 |
|
| 1982 |
Keepers JW, Kollman PA, Weiner PK, James TL. Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings Proceedings of the National Academy of Sciences of the United States of America. 79: 5537-5541. PMID 6957879 DOI: 10.1073/Pnas.79.18.5537 |
0.358 |
|
| 1982 |
Weiner PK, Langridge R, Blaney JM, Schaefer R, Kollman PA. Electrostatic potential molecular surfaces. Proceedings of the National Academy of Sciences of the United States of America. 79: 3754-8. PMID 6285364 DOI: 10.1073/Pnas.79.12.3754 |
0.313 |
|
| 1982 |
Blaney JM, Weiner PK, Dearing A, Kollman PA, Jorgensen EC, Oatley SJ, Burridge JM, Blake CCF. Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin Journal of the American Chemical Society. 104: 6424-6434. DOI: 10.1021/Ja00387A046 |
0.328 |
|
| 1982 |
Wipff G, Weiner P, Kollman P. A molecular-mechanics study of 18-crown-6 and its alkali complexes: an analysis of structural flexibility, ligand specificity, and the macrocyclic effect Journal of the American Chemical Society. 104: 3249-3258. DOI: 10.1021/Ja00376A001 |
0.323 |
|
| 1982 |
Kollman P, Dearing A, Kochanski E. Ab initio self-consistent field calculations on molecular iodine-ammonia and hydrogen iodide-ammonia. The classic "charge-transfer" interaction, an example of gas-phase proton transfer, and the duality of Lewis acid sites on hydrogen iodide The Journal of Physical Chemistry. 86: 1607-1610. DOI: 10.1021/J100206A026 |
0.326 |
|
| 1982 |
Profeta SJ, Kollman PA, Wolff ME. Conformation Of The Progesterone Side Chain: Resolution Of The Apparent Conflict Between X‐Ray Data And Force‐Field Calculations Using Mm2 Journal of the American Chemical Society. 13: 3745-3747. DOI: 10.1002/Chin.198242068 |
0.318 |
|
| 1982 |
Kollman P, Keepers JW, Weiner P. Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting Biopolymers. 21: 2345-2376. DOI: 10.1002/Bip.360211204 |
0.413 |
|
| 1981 |
Kollman PA, Weiner PK, Dearing A. Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers. Biopolymers. 20: 2583-2621. PMID 7326360 DOI: 10.1002/Bip.1981.360201208 |
0.342 |
|
| 1981 |
Dearing A, Weiner P, Kollman PA. Molecular mechanical studies of proflavine and acridine orange intercalation Nucleic Acids Research. 9: 1483-1498. PMID 7232221 DOI: 10.1093/Nar/9.6.1483 |
0.357 |
|
| 1981 |
Kollman PA, Weiner PK, Dearing A. Theoretical Studies Of The Structure And Energies Of Base‐Paired Nucleotides And The Dissociation Kinetics Of A Proflavine‐Dinucleotide Complex* Annals of the New York Academy of Sciences. 367: 250-268. PMID 6942754 DOI: 10.1111/J.1749-6632.1981.Tb50572.X |
0.398 |
|
| 1981 |
Lybrand T, Dearing A, Weiner P, Kollman P. A molecular mechanical study of complexes formed between 4-nitroquinoline-N-oxide and dinucleoside phosphates. Nucleic Acids Research. 9: 6995-7011. PMID 6801629 DOI: 10.1093/Nar/9.24.6995 |
0.335 |
|
| 1981 |
Kollman PA, Hayes DM. Theoretical calculations on proton-transfer energetics: studies of methanol, imidazole, formic acid, and methaneethiol as models for the serine and cysteine proteases Journal of the American Chemical Society. 103: 2955-2961. DOI: 10.1021/Ja00401A008 |
0.316 |
|
| 1981 |
Weiner PK, Kollman PA. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions Journal of Computational Chemistry. 2: 287-303. DOI: 10.1002/Jcc.540020311 |
0.344 |
|
| 1980 |
Cohen FE, Sternberg MJ, Phillips DC, Kuntz ID, Kollman PA. A diffusion--collision--adhesion model for the kinetics of myoglobin refolding. Nature. 286: 632-4. PMID 7402344 DOI: 10.1038/286632A0 |
0.523 |
|
| 1979 |
Andrea TA, Dietrich SW, Murray WJ, Kollman PA, Jorgensen EC, Rothenberg S. A model for thyroid hormone--receptor interactions. Journal of Medicinal Chemistry. 22: 221-32. PMID 218011 DOI: 10.1021/Jm00189A002 |
0.312 |
|
| 1979 |
Nuss ME, Kollman PA. Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions. Journal of Medicinal Chemistry. 22: 1517-24. PMID 94094 DOI: 10.1021/Jm00198A016 |
0.352 |
|
| 1979 |
Nuss ME, Marsh FJ, Kollman PA. Theoretical studies of drug-dinucleotide interactions. Empirical energy function calculations on the interaction of ethidium, 9-aminoacridine, and proflavin cations with the base-paired dinucleotides GpC and CpG Journal of the American Chemical Society. 101: 825-833. DOI: 10.1021/Ja00498A008 |
0.344 |
|
| 1979 |
Kuntz ID, Crippen GM, Kollman PA. Application of distance geometry to protein tertiary structure calculations Biopolymers. 18: 939-957. DOI: 10.1002/Bip.1979.360180414 |
0.603 |
|
| 1978 |
Wolff ME, Baxter JD, Kollman PA, Lee DL, Kuntz ID, Bloom E, Matulich DT, Morris J. Nature of steroid-glucocorticoid receptor interactions: thermodynamic analysis of the binding reaction. Biochemistry. 17: 3201-8. PMID 567487 DOI: 10.1021/Bi00609A005 |
0.512 |
|
| 1978 |
Trenary M, Schaefer HF, Kollman PA. Electronic structure of Li–H2O and related neutral molecular complexes, including Al–H2O The Journal of Chemical Physics. 68: 4047-4050. DOI: 10.1063/1.436305 |
0.371 |
|
| 1978 |
Craig JC, Kollman PA, Lee S-C, Moore RE, Pettus JA, Rothenberg S. Chiroptical properties and optical and molecular orbital calculations for dictyopterenes A and B Journal of the Chemical Society-Perkin Transactions 1. 10: 1338-1344. DOI: 10.1039/P29780001338 |
0.341 |
|
| 1978 |
Hayes DM, Kenyon GL, Kollman PA. Theoretical calculations of the hydrolysis energies of some "high-energy" molecules. 2. A survey of some biologically important hydrolytic reactions Journal of the American Chemical Society. 100: 4331-4340. DOI: 10.1021/Ja00482A002 |
0.371 |
|
| 1978 |
Kollman P, Nelson S, Rothenberg S. The structure and relative energies of C2H2X+ isomers (X = fluoro, hydroxyl, amino, chloro, and mercapto) The Journal of Physical Chemistry. 82: 1403-1406. DOI: 10.1021/J100501A017 |
0.336 |
|
| 1978 |
Douglas JE, Kenyon GL, Kollman PA. The ammonia-sulfur trioxide interaction. An ab initio study Chemical Physics Letters. 57: 553-556. DOI: 10.1016/0009-2614(78)85319-6 |
0.366 |
|
| 1977 |
Kollman P, Kuntz I. Additions and Corrections - Hydration of NH4F Journal of the American Chemical Society. 99: 3894-3894. DOI: 10.1021/Ja00453A603 |
0.517 |
|
| 1977 |
Kollman PA, Kenyon GL. Relative energies of diprotonation of small neutral molecules Journal of the American Chemical Society. 99: 1892-1895. DOI: 10.1021/Ja00448A034 |
0.349 |
|
| 1977 |
Kollman P, Rothenberg S. Theoretical studies of basicity. Proton affinities, lithium(1+) ion affinities, and hydrogen-bond affinities of some simple bases Journal of the American Chemical Society. 99: 1333-1342. DOI: 10.1021/Ja00447A008 |
0.301 |
|
| 1977 |
Kollman P, Rothenberg S. Theoretical Studies Of Basicity. Proton Affinities, Lithium(1+) Ion Affinities, And Hydrogen-Bond Affinities Of Some Simple Bases Cheminform. 8. DOI: 10.1002/Chin.197720103 |
0.301 |
|
| 1977 |
KOLLMAN P, KUNTZ I. ChemInform Abstract: HYDRATION OF AMMONIUM FLUORIDE Chemischer Informationsdienst. 8: no-no. DOI: 10.1002/Chin.197705003 |
0.513 |
|
| 1976 |
Hayes DM, Kollman PA. Electrostatic potentials of proteins. 2. Role of electrostatics in a possible catalytic mechanism for carboxypeptidase A. Journal of the American Chemical Society. 98: 7811-4. PMID 993499 DOI: 10.1021/Ja00440A057 |
0.3 |
|
| 1976 |
Kuntz ID, Crippen GM, Kollman PA, Kimelman D. Calculation of protein tertiary structure Journal of Molecular Biology. 106: 983-994. PMID 978745 DOI: 10.1016/0022-2836(76)90347-8 |
0.584 |
|
| 1976 |
Kollman P, Kuntz I. Hydration of ammonium fluoride Journal of the American Chemical Society. 98: 6820-6825. DOI: 10.1021/Ja00438A007 |
0.519 |
|
| 1975 |
Hayes DM, Kenyon GL, Kollman PA. Theoretical calculations of the hydrolysis energies of some high energy molecules. I. Phosphoric and carboxylic acid anhydrides Journal of the American Chemical Society. 97: 4762-4763. DOI: 10.1021/Ja00849A052 |
0.381 |
|
| 1974 |
Kollman PA, Kuntz ID. Hydration number of lithium(1+) ion Journal of the American Chemical Society. 96: 4766-4769. DOI: 10.1021/Ja00822A007 |
0.479 |
|
| 1974 |
Johansson A, Kollman PA, Liebman JF, Rothenberg S. Substituent effects on proton affinities of simple molecules Journal of the American Chemical Society. 96: 3750-3754. DOI: 10.1021/Ja00819A006 |
0.495 |
|
| 1974 |
Kollman P, Johansson A, Rothenberg S. HCl and HF proton donors: a theoretical study Chemical Physics Letters. 24: 199-202. DOI: 10.1016/0009-2614(74)85432-1 |
0.357 |
|
| 1974 |
Kollman PA, Bender CF, McKelvey J. The rotational barrier in dimethyl acetylene and related molecules Chemical Physics Letters. 28: 407-411. DOI: 10.1016/0009-2614(74)80378-7 |
0.32 |
|
| 1973 |
Kollman PA, Giannini DD, Duax WL, Rothenberg S, Wolff ME. Quantitation of long-range effects in steroids by molecular orbital calculations Journal of the American Chemical Society. 95: 2869-2873. PMID 4694715 DOI: 10.1021/Ja00790A022 |
0.321 |
|
| 1973 |
Johansson A, Kollman P, Rothenberg S. An ab initio molecular orbital study of intramolecular H-bonding: 1,3 propanediol Chemical Physics Letters. 18: 276-279. DOI: 10.1016/0009-2614(73)80436-1 |
0.362 |
|
| 1973 |
Kollman PA, Bender CF. The structure of the H3O+ (hydronium) ion Chemical Physics Letters. 21: 271-274. DOI: 10.1016/0009-2614(73)80133-2 |
0.336 |
|
| 1973 |
KOLLMAN PA, KUNTZ ID. ChemInform Abstract: HYDRATATION VON KATIONEN Chemischer Informationsdienst. 4: no-no. DOI: 10.1002/Chin.197310019 |
0.511 |
|
| 1972 |
Kollman PA, Allen LC. Theory of the hydrogen bond Chemical Reviews. 72: 283-303. DOI: 10.1021/Cr60277A004 |
0.504 |
|
| 1972 |
Johansson A, Kollman P, Rothenberg S. Hydrogen bonding and the structure of the HFHCN dimer Chemical Physics Letters. 16: 123-127. DOI: 10.1016/0009-2614(72)80472-X |
0.351 |
|
| 1972 |
Johansson A, Kollman P, Rothenberg S. The electronic structure of the HCN dimer and trimer Theoretical Chemistry Accounts. 26: 97-100. DOI: 10.1007/Bf00527658 |
0.34 |
|
| 1971 |
Allen LC, Kollman PA. Theoretical evidence against the existence of polywater. Nature. 233: 550-1. PMID 16063494 DOI: 10.1038/233550A0 |
0.476 |
|
| 1971 |
Kollman PA, Allen LC. The nature of the hydrogen bond. Dimers involving electronegative atoms of the first row Journal of the American Chemical Society. 93: 4991-5000. DOI: 10.1021/Ja00749A002 |
0.516 |
|
| 1970 |
Allen LC, Kollman PA. A theory of anomalous water. Science (New York, N.Y.). 167: 1443-54. PMID 17750335 DOI: 10.1126/Science.167.3924.1443 |
0.483 |
|
| 1970 |
Kollman PA, Allen LC. Theory of the hydrogen bond: ab initio calculations on hydrogen fluoride dimer and the mixed water-hydrogen fluoride dimer The Journal of Chemical Physics. 52: 5085-5094. DOI: 10.1063/1.1672746 |
0.6 |
|
| 1970 |
Kollman PA, Allen LC. Theory of the strong hydrogen bond. Ab initio calculations on HF2- and H5O2+1a Journal of the American Chemical Society. 92: 6101-6107. DOI: 10.1021/Ja00724A001 |
0.531 |
|
| 1970 |
Allen LC, Kollman PA. Cyclic systems containing divalent hydroen symmetrically placed between sp2 hybridized electron-rich atoms. A new form of chemical bong? Journal of the American Chemical Society. 92: 4108-4110. DOI: 10.1021/Ja00716A050 |
0.493 |
|
| 1970 |
Kollman PA, Allen LC. Hydrogen bonded dimers and polymers involving hydrogen fluoride, water, and ammonia Journal of the American Chemical Society. 92: 753-759. DOI: 10.1021/Ja00707A002 |
0.509 |
|
| 1969 |
Kollman PA, Allen LC. Theory of the Hydrogen Bond: Electronic Structure and Properties of the Water Dimer Journal of Chemical Physics. 51: 3286-3293. DOI: 10.1063/1.1672509 |
0.574 |
|
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