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Peter Kollman

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Amino Acid Sequence

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Co-Publications
Name
12
Cheatham, Thomas
12
Kuntz, Irwin
7
Kuhn, Bernd
6
Reyes, CM
6
Wang, Junmei
5
Cieplak, Piotr
4
Cooke, Roger
4
Donini, OA
4
Wang, W
4
Minehardt, Todd
4
Massova, Irina
4
Pate, Edward
4
Pitera, JW
4
Brooks, Bernard
3
Luo, Ray

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Publications

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

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All Publications

2006: Yang Lijiang; Tan Chun-Hu; Hsieh Meng-Juei; Wang Junmei; Duan Yong; Cieplak Piotr; Caldwell James; Kollman Peter A; Luo Ray
New-generation amber united-atom force field.
The journal of physical chemistry. B 2006;110(26):13166-76.
2006: Minehardt T J; Kollman P A; 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 2006;90(7):2445-9.
2004: Kuhn Bernd; Kollman Peter A; Stahl Martin
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: Wen Edward Z; Hsieh Meng-Juei; Kollman Peter A; Luo Ray
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: Duan Yong; Wu Chun; Chowdhury Shibasish; Lee Mathew C; Xiong Guoming; Zhang Wei; Yang Rong; Cieplak Piotr; Luo Ray; Lee Taisung; Caldwell James; Wang Junmei; Kollman Peter
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: Chong Lillian T; Bandyopadhyay Pradipta; Scanlan Thomas S; Kuntz Irwin D; Kollman Peter A
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9.
Journal of computational chemistry 2003;24(12):1371-7.
2003: Naber Nariman; Minehardt Todd J; Rice Sarah; Chen Xiaoru; Grammer Jean; Matuska Marija; Vale Ronald D; Kollman Peter A; Car Roberto; Yount Ralph G; Cooke Roger; Pate Edward
Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules.
Science (New York, N.Y.) 2003;300(5620):798-801.
2003: Gouda Hiroaki; Kuntz Irwin D; Case David A; Kollman Peter A
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: Massova Irina; Kollman Peter A
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: Asada Toshio; Gouda Hiroaki; Kollman Peter A
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: Mooney Sean D; Kollman Peter A; Klein Teri E
Conformational preferences of substituted prolines in the collagen triple helix.
Biopolymers 2002;64(2):63-71.
2002: Huo Shuanghong; Wang Junmei; Cieplak Piotr; Kollman Peter A; Kuntz Irwin D
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: Dixon Richard W; Radmer Randall J; Kuhn Bernd; Kollman Peter A; Yang Jaemoon; Raposo Cesar; Wilcox Craig S; Klumb Lisa A; Stayton Patrick S; Behnke Craig; Le Trong Isolde; Stenkamp Ronald
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: Minehardt Todd J; Marzari Nicola; Cooke Roger; Pate Edward; Kollman Peter A; Car Roberto
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: Huo Shuanghong; Massova Irina; Kollman Peter A
Computational alanine scanning of the 1:1 human growth hormone-receptor complex.
Journal of computational chemistry 2002;23(1):15-27.
2001: Wang W; Kollman P A
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: Lee T S; Chong L T; Chodera J D; Kollman P A
An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.
Journal of the American Chemical Society 2001;123(51):12837-48.
2001: Cheatham T E; Brooks B R; Kollman P A
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: Cheatham T E; Brooks B R; Kollman P A
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: Lee M R; Tsai J; Baker D; Kollman P A
Molecular dynamics in the endgame of protein structure prediction.
Journal of molecular biology 2001;313(2):417-30.
2001: Lee M R; Kollman P A
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: Krueger B P; Kollman P A
Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship.
Proteins 2001;45(1):4-15.
2001: Cheatham T E; Brooks B R; Kollman P A
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: Wang J; Morin P; Wang W; Kollman P A
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: Kuhn B; Jacobsen W; Christians U; Benet L Z; Kollman P A
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: Reyes C M; Nifosì R; Frankel A D; Kollman P A
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex.
Biophysical journal 2001;80(6):2833-42.
2001: Cheatham T E; Brooks B R; Kollman P A
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: Wang W; Lim W A; Jakalian A; Wang J; Wang J; Luo R; Bayly C I; Kollman P A
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: Minehardt T J; Cooke R; Pate E; Kollman P A
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: Mooney S D; Huang C C; Kollman P A; Klein T E
Computed free energy differences between point mutations in a collagen-like peptide.
Biopolymers 2001;58(3):347-53.
2001: Lee M R; Baker D; Kollman P A
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: Wang L; Duan Y; Stouten P; De Lucca G V; Klabe R M; Kollman P A
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: Kollman P A; 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 2001;34(1):72-9.
2001: Lee M R; Duan Y; Kollman P A
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: Wang W; Donini O; Reyes C M; Kollman P A
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.
2000: Kollman P A; 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 D A; Cheatham T E
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
Accounts of chemical research 2000;33(12):889-97.
2000: Nifosì R; Reyes C M; Kollman P A
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide.
Nucleic acids research 2000;28(24):4944-55.
2000: Donini O A; Kollman P A
Calculation and prediction of binding free energies for the matrix metalloproteinases.
Journal of medicinal chemistry 2000;43(22):4180-8.
2000: Wang W; Kollman P A
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: Jacobsen W; Kuhn B; Soldner A; Kirchner G; Sewing K F; Kollman P A; Benet L Z; Christians U
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: Pitera J W; Kollman P A
Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
Proteins 2000;41(3):385-97.
2000: Kuhn B; Kollman P A
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: Lee M R; Duan Y; Kollman P A
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: Reyes C M; Kollman P A
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: Reyes C M; Kollman P A
Investigating the binding specificity of U1A-RNA by computational mutagenesis.
Journal of molecular biology 2000;295(1):1-6.
2000: Cheatham T E; Kollman P A
Molecular dynamics simulation of nucleic acids.
Annual review of physical chemistry 2000;51():435-71.
1999: Chong L T; Duan Y; Wang L; Massova I; Kollman P A
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: Dixon R W; 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 1999;36(4):471-3.
1999: Kuntz I D; Chen K; Sharp K A; Kollman P A
The maximal affinity of ligands.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(18):9997-10002.
1999: Pitera J W; Munagala N R; Wang C C; Kollman P A
Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment.
Biochemistry 1999;38(32):10298-306.
1999: Kollman P A
Hydrogen bonding.
Current biology : CB 1999;9(14):R501.
1999: Wang J; Kollman P A; Kuntz I D
Flexible ligand docking: a multistep strategy approach.
Proteins 1999;36(1):1-19.
1999: Wang L; Duan Y; Shortle R; Imperiali B; Kollman P A
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: Eriksson M A; Pitera J; Kollman P A
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: Cheatham T E; Cieplak P; Kollman P A
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: Konerding D E; Cheatham T E; Kollman P A; James T L
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method.
Journal of biomolecular NMR 1999;13(2):119-31.
1999: Reyes C M; Kollman P A
Molecular dynamics studies of U1A-RNA complexes.
RNA (New York, N.Y.) 1999;5(2):235-44.
1999: Wang W; Wang J; Kollman P A
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: Wang J; Dixon R; Kollman P A
Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.
Proteins 1999;34(1):69-81.
1998: Cheatham T E; Srinivasan J; Case D A; Kollman P A
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: Duan Y; Kollman P A
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: Wang L; Veenstra D L; Radmer R J; Kollman P A
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: Duan Y; Wang L; Kollman P A
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: Radmer R J; Kollman P A
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: Pitera J; Kollman P
Graphical visualization of mean hydration from molecular dynamics simulations.
Journal of molecular graphics & modelling 1997;15(6):355-8, 386-8.
1997: Cheatham T E; Kollman P A
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: Cheatham T E; Crowley M F; Fox T; Kollman P A
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: Veenstra D L; Kollman P A
Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants.
Protein engineering 1997;10(7):789-807.
1997: Miller J L; Kollman P A
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.
1996: Fox T; Kollman P A
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: Cheatham T E; Kollman P A
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: Cieplak P; Kollman P A
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: Sun Y C; Veenstra D L; Kollman P A
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: Grootenhuis P D; Roe D C; Kollman P A; Kuntz I D
Finding potential DNA-binding compounds by using molecular shape.
Journal of computer-aided molecular design 1994;8(6):731-50.
1994: Cornish V W; Kaplan M I; Veenstra D L; Kollman P A; Schultz P G
Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices.
Biochemistry 1994;33(40):12022-31.
1994: Singh S B; Wemmer D E; Kollman P A
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: Guenot J; Fletterick R J; Kollman P A
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: McCarrick M A; Kollman P
Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design.
Methods in enzymology 1994;241():370-84.
1993: Singh S B; Pearlman D A; Kollman P A
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: Miyamoto S; Kollman P A
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: Miyamoto S; Kollman P A
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: Cieplak P; Kollman P A
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: Guenot J; Kollman P A
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: Howard A E; Kollman P A
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: Mendel D; Ellman J A; Chang Z; Veenstra D L; Kollman P A; Schultz P G
Probing protein stability with unnatural amino acids.
Science (New York, N.Y.) 1992;256(5065):1798-802.
1992: Dahl S G; Kollman P A; Rao S N; Singh U C
Structural changes by sulfoxidation of phenothiazine drugs.
Journal of computer-aided molecular design 1992;6(3):207-22.
1992: Schiffer C A; Caldwell J W; Stroud R M; Kollman P A
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: Hurle M R; Eads C D; Pearlman D A; Seibel G L; Thomason J; Kosen P A; Kollman P; Anderson S; Kuntz I D
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: Daggett V; Kollman P A; Kuntz I D
A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions.
Biopolymers 1991;31(9):1115-34.
1991: Ferguson D M; Radmer R J; Kollman P A
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: Pearlman D A; Kollman P A
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: Mizushima N; Spellmeyer D; Hirono S; Pearlman D; Kollman P
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: Kollman P A; Dill K A
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: Daggett V; Kollman P A; Kuntz I D
Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.
Biopolymers 1991;31(3):285-304.
1991: Hirono S; Kollman P A
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: Caldwell J W; Agard D A; Kollman P A
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: Daggett V; Kollman P A
Molecular dynamics simulations of active site mutants of triosephosphate isomerase.
Protein engineering 1990;3(8):677-90.
1990: Grootenhuis P D; Kollman P A; Seibel G L; DesJarlais R L; Kuntz I D
Computerized selection of potential DNA binding compounds.
Anti-cancer drug design 1990;5(3):237-42.
1990: Pearlman D A; Kollman P A
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: Rao S N; Kollman P A
Conformations of deoxydinucleoside phosphates containing pyrimidine-pyrimidine photodimers.
Indian journal of biochemistry & biophysics 1990;27(3):130-5.
1990: Dang L X; Pearlman D A; Kollman P A
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: Chiche L; Gregoret L M; Cohen F E; Kollman P A
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: Cieplak P; Rao S N; Grootenhuis P D; Kollman P A
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: Hirono S; Kollman P A
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: Rao S N; 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 1990;29(3):517-32.
1990: Schiffer C A; Caldwell J W; Kollman P A; Stroud R M
Prediction of homologous protein structures based on conformational searches and energetics.
Proteins 1990;8(1):30-43.
1989: Creighton S; Rudolph B; Lybrand T; Singh U C; Shafer R; Brown S; Kollman P; Case D A; 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 1989;6(5):929-69.
1989: Rao S N; Lybrand T; Michaud D; Jerina D M; Kollman P A
Molecular mechanics simulations on covalent complexes between polycyclic carcinogens and B-DNA.
Carcinogenesis 1989;10(1):27-38.
1989: Chiche L; Gaboriaud C; Heitz A; Mornon J P; Castro B; Kollman P A
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: Howard A E; Kollman P A
An analysis of current methodologies for conformational searching of complex molecules.
Journal of medicinal chemistry 1988;31(9):1669-75.
1988: Tilton R F; Singh U C; Kuntz I D; Kollman P A
Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex.
Journal of molecular biology 1988;199(1):195-211.
1988: Caldwell J W; Kollman P A
Investigation of the substrate binding and phosphate transfer in adenylate kinase by molecular mechanics.
Enzyme 1988;39(2):61-77.
1987: Brown F K; Kollman P A
Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase.
Journal of molecular biology 1987;198(3):533-46.
1987: Cieplak P; Rao S N; Hélène C; Montenay-Garestier T; Kollman P A
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: Rao S N; Singh U C; Bash P A; Kollman P A
Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin.
Nature 1987;328(6130):551-4.
1987: Behling R W; Rao S N; Kollman P; Kearns D R
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: Bash P A; Singh U C; Langridge R; Kollman P A
Free energy calculations by computer simulation.
Science (New York, N.Y.) 1987;236(4801):564-8.
1987: Pattabiraman N; Rao S N; Scott K; Langridge R; Kollman P A
Molecular mechanical studies on left- and right-handed B-DNA.
Biopolymers 1987;26(3):403-14.
1987: Bash P A; Singh U C; Brown F K; Langridge R; Kollman P A
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: Rao S N; Singh U C; Kollman P A
Molecular mechanics simulations on covalent complexes between anthramycin and B DNA.
Journal of medicinal chemistry 1986;29(12):2484-92.
1986: Tilton R F; Singh U C; Weiner S J; Connolly M L; Kuntz I D; Kollman P A; Max N; Case D A
Computational studies of the interaction of myoglobin and xenon.
Journal of molecular biology 1986;192(2):443-56.
1986: Lybrand T P; Brown S C; Creighton S; Shafer R H; Kollman P A
Computer modeling of actinomycin D interactions with double-helical DNA.
Journal of molecular biology 1986;191(3):495-507.
1986: Singh U C; Pattabiraman N; Langridge R; Kollman P A
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: Remers W A; Rao S N; Singh U C; Kollman P A
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: Haasnoot C A; Hilbers C W; van der Marel G A; van Boom J H; Singh U C; Pattabiraman N; Kollman P A
On loop folding in nucleic acid hairpin-type structures.
Journal of biomolecular structure & dynamics 1986;3(5):843-57.
1986: Weiner S J; Seibel G L; Kollman P A
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: Kollman P A; Weiner S; Seibel G; Lybrand T; Singh U C; Caldwell J; Rao S N
Modeling complex molecular interactions involving proteins and DNA.
Annals of the New York Academy of Sciences 1986;482():234-44.
1985: Lybrand T; Kollman P
Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA.
Biopolymers 1985;24(10):1863-79.
1985: Seibel G L; Singh U C; Kollman P A
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: Caldwell J W; Kollman P A
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: Singh U C; Weiner S J; Kollman P
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: Pattabiraman N; Langridge R; Kollman P A
An iterative approach to placing counterions around DNA.
Journal of biomolecular structure & dynamics 1984;1(6):1525-33.
1981: Kollman P A; Weiner P K; Dearing A
Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers.
Biopolymers 1981;20(12):2583-621.
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 1981;9(24):6995-7011.
1981: Dearing A; Weiner P; Kollman P A
Molecular mechanical studies of proflavine and acridine orange intercalation.
Nucleic acids research 1981;9(6):1483-97.
1981: Kollman P A; Weiner P K; 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 1981;367():250-68.

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