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Peter Kollman

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TOP 3
Lijiang Yang; Chun-Hu Tan; Meng-Juei Hsieh; Junmei Wang; Yong Duan; Piotr Cieplak; James Caldwell; Peter A Kollman; Ray Luo
New-generation amber united-atom force field.
Todd J Minehardt; Peter A Kollman; Roger Cooke; Edward Pate
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
Bernd Kuhn; Peter A Kollman; Martin Stahl
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.

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2006: Lijiang Yang; Chun-Hu Tan; Meng-Juei Hsieh; Junmei Wang; Yong Duan; Piotr Cieplak; James Caldwell; Peter A Kollman; Ray Luo
New-generation amber united-atom force field.
The journal of physical chemistry. B 2006;110(26):13166-76.
2006: Todd J Minehardt; Peter A Kollman; Roger Cooke; Edward Pate
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
Biophysical journal 2006;90(7):2445-9.
2004: Bernd Kuhn; Peter A Kollman; Martin Stahl
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.
Journal of computational chemistry 2004;25(15):1865-72.
2004: Edward Z Wen; Meng-Juei Hsieh; Peter A Kollman; Ray Luo
Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces.
Journal of molecular graphics & modelling 2004;22(5):415-24.
2003: Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter A Kollman
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Journal of computational chemistry 2003;24(16):1999-2012.
2003: Lillian T Chong; Pradipta Bandyopadhyay; Thomas S Scanlan; Irwin D Kuntz; Peter A Kollman
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9.
Journal of computational chemistry 2003;24(12):1371-7.
2003: Nariman Naber; Todd J Minehardt; Sarah Rice; Xiaoru Chen; Jean Grammer; Marija Matuska; Ronald D Vale; Peter A Kollman; Roberto Car; Ralph G Yount; Roger Cooke; Edward Pate
Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules.
Science (New York, N.Y.) 2003;300(5620):798-801.
2003: Hiroaki Gouda; Irwin D Kuntz; David A Case; Peter A Kollman
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods.
Biopolymers 2003;68(1):16-34.
2002: Irina Massova; Peter A Kollman
pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step.
Journal of computational chemistry 2002;23(16):1559-76.
2002: Toshio Asada; Hiroaki Gouda; Peter A Kollman
Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement.
Journal of the American Chemical Society 2002;124(42):12535-42.
2002: Sean D Mooney; Peter A Kollman; Teri E Klein
Conformational preferences of substituted prolines in the collagen triple helix.
Biopolymers 2002;64(2):63-71.
2002: Shuanghong Huo; Junmei Wang; Piotr Cieplak; Peter A Kollman; Irwin D Kuntz
Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design.
Journal of medicinal chemistry 2002;45(7):1412-9.
2002: Richard W Dixon; Randall J Radmer; Bernd Kuhn; Peter A Kollman; Jaemoon Yang; Cesar Raposo; Craig S Wilcox; Lisa A Klumb; Patrick S Stayton; Craig Behnke; Isolde Le Trong; Ronald E Stenkamp
Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin.
The Journal of organic chemistry 2002;67(6):1827-37.
2002: Todd J Minehardt; Nicola Marzari; Roger Cooke; Edward Pate; Peter A Kollman; Roberto Car
A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.
Biophysical journal 2002;82(2):660-75.
2002: Shuanghong Huo; Irina Massova; Peter A Kollman
Computational alanine scanning of the 1:1 human growth hormone-receptor complex.
Journal of computational chemistry 2002;23(1):15-27.
2001: T S Lee; Lillian T Chong; J D Chodera; Peter A Kollman
An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.
Journal of the American Chemical Society 2001;123(51):12837-48.
2001: W Wang; Peter A Kollman
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 2001;98(26):14937-42.
2001: Thomas E Cheatham; Bernard Brooks; Peter A Kollman
Molecular modeling of nucleic acid structure.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2001;Chapter 7():Unit 7.5.
2001: Thomas E Cheatham; Bernard Brooks; Peter A Kollman
Molecular modeling of nucleic acid structure: setup and analysis.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2001;Chapter 7():Unit 7.10.
2001: M R Lee; J Tsai; D Baker; Peter A Kollman
Molecular dynamics in the endgame of protein structure prediction.
Journal of molecular biology 2001;313(2):417-30.
2001: M R Lee; Peter A Kollman
Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction.
Structure (London, England : 1993) 2001;9(10):905-16.
2001: B P Krueger; Peter A Kollman
Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship.
Proteins 2001;45(1):4-15.
2001: Thomas E Cheatham; Bernard Brooks; Peter A Kollman
Molecular modeling of nucleic acid structure: electrostatics and solvation.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2001;Chapter 7():Unit 7.9.
2001: Bernd Kuhn; Wolfgang Jacobsen; Uwe Christians; Leslie Z Benet; Peter A Kollman
Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations.
Journal of medicinal chemistry 2001;44(12):2027-34.
2001: Junmei Wang; P Morin; W Wang; Peter A Kollman
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 2001;123(22):5221-30.
2001: CM Reyes; Riccardo Nifosì; Alan D Frankel; Peter A Kollman
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex.
Biophysical journal 2001;80(6):2833-42.
2001: W Wang; Wendell A Lim; Araz Jakalian; Junmei Wang; J Wang; R Luo; Christopher I Bayly; Peter A Kollman
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 2001;123(17):3986-94.
2001: Thomas E Cheatham; Bernard Brooks; Peter A Kollman
Molecular modeling of nucleic acid structure: energy and sampling.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2001;Chapter 7():Unit 7.8.
2001: Todd J Minehardt; Roger Cooke; Edward Pate; Peter A Kollman
Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd.
Biophysical journal 2001;80(3):1151-68.
2001: Sean D Mooney; C C Huang; Peter A Kollman; Teri E Klein
Computed free energy differences between point mutations in a collagen-like peptide.
Biopolymers 2001;58(3):347-53.
2001: M R Lee; D Baker; Peter A Kollman
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 2001;123(6):1040-6.
2001: L Wang; Y Duan; P Stouten; George V De Lucca; Ronald Klabe; Peter A Kollman
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 2001;15(2):145-56.
2001: M R Lee; Y Duan; Peter A Kollman
State of the art in studying protein folding and protein structure prediction using molecular dynamics methods.
Journal of molecular graphics & modelling 2001;19(1):146-9.
2001: W Wang; OA Donini; CM Reyes; Peter A Kollman
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 2001;30():211-43.
2001: Peter A Kollman; Bernd Kuhn; OA Donini; M Perakyla; R Stanton; D Bakowies
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 2001;34(1):72-9.
2000: Riccardo Nifosì; CM Reyes; Peter A Kollman
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide.
Nucleic acids research 2000;28(24):4944-55.
2000: Peter A Kollman; Irina Massova; C Reyes; Bernd Kuhn; Shuanghong Huo; L Chong; M Lee; T Lee; Y Duan; W Wang; OA Donini; Piotr Cieplak; J Srinivasan; David A Case; Thomas E Cheatham
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
Accounts of chemical research 2000;33(12):889-97.
2000: JW Pitera; Peter A Kollman
Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
Proteins 2000;41(3):385-97.
2000: W Wang; Peter A Kollman
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model.
Journal of molecular biology 2000;303(4):567-82.
2000: OA Donini; Peter A Kollman
Calculation and prediction of binding free energies for the matrix metalloproteinases.
Journal of medicinal chemistry 2000;43(22):4180-8.
2000: Wolfgang Jacobsen; Bernd Kuhn; A Soldner; Gabriele I Kirchner; KF Sewing; Peter A Kollman; Leslie Z Benet; Uwe Christians
Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin.
Drug metabolism and disposition: the biological fate of chemicals 2000;28(11):1369-78.
2000: Bernd Kuhn; Peter A Kollman
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 2000;43(20):3786-91.
2000: M R Lee; Y Duan; Peter A Kollman
Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece.
Proteins 2000;39(4):309-16.
2000: CM Reyes; Peter A Kollman
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 2000;297(5):1145-58.
2000: CM Reyes; Peter A Kollman
Investigating the binding specificity of U1A-RNA by computational mutagenesis.
Journal of molecular biology 2000;295(1):1-6.
2000: Thomas E Cheatham; Peter A Kollman
Molecular dynamics simulation of nucleic acids.
Annual review of physical chemistry 2000;51():435-71.
1999: Lillian T Chong; Y Duan; L Wang; Irina Massova; Peter A Kollman
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 1999;96(25):14330-5.
1999: R W Dixon; Peter A Kollman
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 1999;36(4):471-3.
1999: Irwin D Kuntz; K Chen; K A Sharp; Peter A Kollman
The maximal affinity of ligands.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(18):9997-10002.
1999: JW Pitera; Narsimha Munagala; Ching C Wang; Peter A Kollman
Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment.
Biochemistry 1999;38(32):10298-306.
1999: Peter A Kollman
Hydrogen bonding.
Current biology : CB 1999;9(14):R501.
1999: J Wang; Peter A Kollman; Irwin D Kuntz
Flexible ligand docking: a multistep strategy approach.
Proteins 1999;36(1):1-19.
1999: L Wang; Y Duan; R Shortle; B Imperiali; Peter A Kollman
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures.
Protein science : a publication of the Protein Society 1999;8(6):1292-304.
1999: M A Eriksson; JW Pitera; Peter A Kollman
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 1999;42(5):868-81.
1999: W Wang; J Wang; Peter A Kollman
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 1999;34(3):395-402.
1999: Thomas E Cheatham; Piotr Cieplak; Peter A Kollman
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.
Journal of biomolecular structure & dynamics 1999;16(4):845-62.
1999: David Konerding; Thomas E Cheatham; Peter A Kollman; Tom L James
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method.
Journal of biomolecular NMR 1999;13(2):119-31.
1999: CM Reyes; Peter A Kollman
Molecular dynamics studies of U1A-RNA complexes.
RNA (New York, N.Y.) 1999;5(2):235-44.
1999: J Wang; R Dixon; Peter A Kollman
Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.
Proteins 1999;34(1):69-81.
1998: Y Duan; Peter A Kollman
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
Science (New York, N.Y.) 1998;282(5389):740-4.
1998: Thomas E Cheatham; J Srinivasan; David A Case; Peter A Kollman
Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.
Journal of biomolecular structure & dynamics 1998;16(2):265-80.
1998: L Wang; D L Veenstra; Randall J Radmer; Peter A Kollman
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 1998;32(4):438-58.
1998: Y Duan; L Wang; Peter A Kollman
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 1998;95(17):9897-902.
1998: Randall J Radmer; Peter A Kollman
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 1998;12(3):215-27.
1997: JW Pitera; Peter A Kollman
Graphical visualization of mean hydration from molecular dynamics simulations.
Journal of molecular graphics & modelling 1997;15(6):355-8, 386-8.
1997: Thomas E Cheatham; Peter A Kollman
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) 1997;5(10):1297-311.
1997: Thomas E Cheatham; M F Crowley; T Fox; Peter A Kollman
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 1997;94(18):9626-30.
1997: Jennifer Miller; Peter A Kollman
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 1997;270(3):436-50.
1997: D L Veenstra; Peter A Kollman
Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants.
Protein engineering 1997;10(7):789-807.
1996: T Fox; Peter A Kollman
The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?
Proteins 1996;25(3):315-34.
1996: Thomas E Cheatham; Peter A Kollman
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution.
Journal of molecular biology 1996;259(3):434-44.
1996: P Cieplak; Peter A Kollman
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 1996;9(2):103-12.
1996: Y C Sun; D L Veenstra; Peter A Kollman
Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability.
Protein engineering 1996;9(3):273-81.
1994: P D Grootenhuis; D C Roe; Peter A Kollman; Irwin D Kuntz
Finding potential DNA-binding compounds by using molecular shape.
Journal of computer-aided molecular design 1994;8(6):731-50.
1994: V W Cornish; M I Kaplan; D L Veenstra; Peter A Kollman; Peter G Schultz
Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices.
Biochemistry 1994;33(40):12022-31.
1994: S B Singh; David E Wemmer; Peter A Kollman
Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(16):7673-7.
1994: J Guenot; Robert J Fletterick; Peter A Kollman
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 1994;3(8):1276-85.
1994: M A McCarrick; Peter A Kollman
Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design.
Methods in enzymology 1994;241():370-84.
1993: S B Singh; D A Pearlman; Peter A Kollman
Free energy component analysis: application to the "Z-phobicity" of A-T base pairs.
Journal of biomolecular structure & dynamics 1993;11(2):303-11.
1993: S Miyamoto; Peter A Kollman
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 1993;90(18):8402-6.
1993: S Miyamoto; Peter A Kollman
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 1993;16(3):226-45.
1993: P Cieplak; Peter A Kollman
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 1993;7(3):291-304.
1992: J Guenot; Peter A Kollman
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 1992;1(9):1185-205.
1992: A E Howard; Peter A Kollman
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 1992;1(9):1173-84.
1992: D Mendel; Jonathan A Ellman; Z Chang; D L Veenstra; Peter A Kollman; Peter G Schultz
Probing protein stability with unnatural amino acids.
Science (New York, N.Y.) 1992;256(5065):1798-802.
1992: Svein G Dahl; Peter A Kollman; S N Rao; U C Singh
Structural changes by sulfoxidation of phenothiazine drugs.
Journal of computer-aided molecular design 1992;6(3):207-22.
1992: C A Schiffer; J W Caldwell; Robert M Stroud; Peter A Kollman
Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.
Protein science : a publication of the Protein Society 1992;1(3):396-400.
1992: M R Hurle; C D Eads; D A Pearlman; G L Seibel; J Thomason; P A Kosen; Peter A Kollman; S Anderson; Irwin D Kuntz
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 1992;1(1):91-106.
1991: V Daggett; Peter A Kollman; Irwin D Kuntz
A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions.
Biopolymers 1991;31(9):1115-34.
1991: D M Ferguson; R J Radmer; Peter A Kollman
Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease.
Journal of medicinal chemistry 1991;34(8):2654-9.
1991: D A Pearlman; Peter A Kollman
Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA.
Journal of molecular biology 1991;220(2):457-79.
1991: N Mizushima; D Spellmeyer; S Hirono; D Pearlman; Peter A Kollman
Free energy perturbation calculations on binding and catalysis after mutating threonine 220 in subtilisin.
The Journal of biological chemistry 1991;266(18):11801-9.
1991: Peter A Kollman; Ken A Dill
Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)).
Journal of biomolecular structure & dynamics 1991;8(6):1103-7; discussion 1109-11.
1991: V Daggett; Peter A Kollman; Irwin D Kuntz
Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.
Biopolymers 1991;31(3):285-304.
1991: S Hirono; Peter A Kollman
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 1991;4(3):233-43.
1991: J W Caldwell; David A Agard; Peter A Kollman
Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket.
Proteins 1991;10(2):140-8.
1990: D A Pearlman; Peter A Kollman
The calculated free energy effects of 5-methyl cytosine on the B to Z transition in DNA.
Biopolymers 1990;29(8-9):1193-209.
1990: V Daggett; Peter A Kollman
Molecular dynamics simulations of active site mutants of triosephosphate isomerase.
Protein engineering 1990;3(8):677-90.
1990: P D Grootenhuis; Peter A Kollman; G L Seibel; R L DesJarlais; Irwin D Kuntz
Computerized selection of potential DNA binding compounds.
Anti-cancer drug design 1990;5(3):237-42.
1990: S N Rao; Peter A Kollman
Conformations of deoxydinucleoside phosphates containing pyrimidine-pyrimidine photodimers.
Indian journal of biochemistry & biophysics 1990;27(3):130-5.
1990: L X Dang; D A Pearlman; Peter A Kollman
Why do A.T base pairs inhibit Z-DNA formation?
Proceedings of the National Academy of Sciences of the United States of America 1990;87(12):4630-4.
1990: L Chiche; Lydia Gregoret; Fred Cohen; Peter A Kollman
Protein model structure evaluation using the solvation free energy of folding.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(8):3240-3.
1990: S Hirono; Peter A Kollman
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 1990;212(1):197-209.
1990: P Cieplak; S N Rao; P D Grootenhuis; Peter A Kollman
Free energy calculation on base specificity of drug--DNA interactions: application to daunomycin and acridine intercalation into DNA.
Biopolymers 1990;29(4-5):717-27.
1990: S N Rao; Peter A Kollman
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 1990;29(3):517-32.
1990: C A Schiffer; J W Caldwell; Peter A Kollman; Robert M Stroud
Prediction of homologous protein structures based on conformational searches and energetics.
Proteins 1990;8(1):30-43.
1989: S Creighton; B Rudolph; T Lybrand; U C Singh; R Shafer; S Brown; Peter A Kollman; D A Case; T Andrea
A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex.
Journal of biomolecular structure & dynamics 1989;6(5):929-69.
1989: S N Rao; T Lybrand; D Michaud; D M Jerina; Peter A Kollman
Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA.
Carcinogenesis 1989;10(1):27-38.
1989: Laurent Chiche; C Gaboriaud; Annie Heitz; Jean-Paul Mornon; B Castro; Peter A Kollman
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 1989;6(4):405-17.
1988: A E Howard; Peter A Kollman
An analysis of current methodologies for conformational searching of complex molecules.
Journal of medicinal chemistry 1988;31(9):1669-75.
1988: R F Tilton; U C Singh; Irwin D Kuntz; Peter A Kollman
Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex.
Journal of molecular biology 1988;199(1):195-211.
1988: J W Caldwell; Peter A Kollman
Investigation of the substrate binding and phosphate transfer in adenylate kinase by molecular mechanics.
Enzyme 1988;39(2):61-77.
1987: F K Brown; Peter A Kollman
Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase.
Journal of molecular biology 1987;198(3):533-46.
1987: P Cieplak; S N Rao; C Hélène; T Montenay-Garestier; Peter A Kollman
Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine.
Journal of biomolecular structure & dynamics 1987;5(2):361-82.
1987: S N Rao; U C Singh; P A Bash; Peter A Kollman
Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin.
Nature 1987;328(6130):551-4.
1987: R W Behling; S N Rao; Peter A Kollman; David R Kearns
Molecular mechanics and dynamics calculations on (dA)10.(dT)10 incorporating distance constraints derived from NMR relaxation measurements.
Biochemistry 1987;26(15):4674-81.
1987: P A Bash; U C Singh; R Langridge; Peter A Kollman
Free energy calculations by computer simulation.
Science (New York, N.Y.) 1987;236(4801):564-8.
1987: N Pattabiraman; S N Rao; K Scott; R Langridge; Peter A Kollman
Molecular mechanical studies on left- and right-handed B-DNA.
Biopolymers 1987;26(3):403-14.
1987: P A Bash; U C Singh; F K Brown; R Langridge; Peter A Kollman
Calculation of the relative change in binding free energy of a protein-inhibitor complex.
Science (New York, N.Y.) 1987;235(4788):574-6.
1986: S N Rao; U C Singh; Peter A Kollman
Molecular mechanics simulations on covalent complexes between anthramycin and B DNA.
Journal of medicinal chemistry 1986;29(12):2484-92.
1986: R F Tilton; U C Singh; Saul J Weiner; M L Connolly; Irwin D Kuntz; Peter A Kollman; N Max; D A Case
Computational studies of the interaction of myoglobin and xenon.
Journal of molecular biology 1986;192(2):443-56.
1986: T P Lybrand; Stephen Brown; S Creighton; R H Shafer; Peter A Kollman
Computer modeling of actinomycin D interactions with double-helical DNA.
Journal of molecular biology 1986;191(3):495-507.
1986: U C Singh; N Pattabiraman; R Langridge; Peter A Kollman
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 1986;83(17):6402-6.
1986: W A Remers; S N Rao; U C Singh; Peter A Kollman
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 1986;29(7):1256-63.
1986: C A Haasnoot; Cornelis W Hilbers; Gijsbert A van der Marel; Jacques H van Boom; U C Singh; N Pattabiraman; Peter A Kollman
On loop folding in nucleic acid hairpin-type structures.
Journal of biomolecular structure & dynamics 1986;3(5):843-57.
1986: Saul J Weiner; G L Seibel; Peter A Kollman
The nature of enzyme catalysis in trypsin.
Proceedings of the National Academy of Sciences of the United States of America 1986;83(3):649-53.
1986: Peter A Kollman; Saul J Weiner; G Seibel; T Lybrand; U C Singh; J Caldwell; S N Rao
Modeling complex molecular interactions involving proteins and DNA.
Annals of the New York Academy of Sciences 1986;482():234-44.
1985: T Lybrand; Peter A Kollman
Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA.
Biopolymers 1985;24(10):1863-79.
1985: G L Seibel; U C Singh; Peter A Kollman
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 1985;82(19):6537-40.
1985: J W Caldwell; Peter A Kollman
The effect of methylation of the 6 oxygen of guanine on the structure and stability of double helical DNA.
Journal of biomolecular structure & dynamics 1985;3(1):57-66.
1985: U C Singh; Saul J Weiner; Peter A Kollman
Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.
Proceedings of the National Academy of Sciences of the United States of America 1985;82(3):755-9.
1984: N Pattabiraman; R Langridge; Peter A Kollman
An iterative approach to placing counterions around DNA.
Journal of biomolecular structure & dynamics 1984;1(6):1525-33.
1981: T Lybrand; A Dearing; P Weiner; Peter A Kollman
A molecular mechanical study of complexes formed between 4-nitroquinoline-N-oxide and dinucleoside phosphates.
Nucleic acids research 1981;9(24):6995-7011.
1981: Peter A Kollman; P K Weiner; A Dearing
Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers.
Biopolymers 1981;20(12):2583-621.
1981: A Dearing; P Weiner; Peter A Kollman
Molecular mechanical studies of proflavine and acridine orange intercalation.
Nucleic acids research 1981;9(6):1483-97.
1981: Peter A Kollman; P K Weiner; A Dearing
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 1981;367():250-68.