Computational Structural Biology
Prof. Amedeo Caflisch

Library screening by fragment-based docking.

J Mol Recognit. 2010 Mar;23(2):183-93

Authors: Huang D, Caflisch A

Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.

Bioinformatics. 2010 Jan 15;26(2):198-204

Authors: Huang D, Zhou T, Lafleur K, Nevado C, Caflisch A

Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles

J. Phys. Chem. Lett., 2010, 1 (2), 471–74

Authors:Friedman R, Pellarin R, Caflisch A

Slow folding of cross-linked alpha-helical peptides due to steric hindrance.

J Phys Chem B. 2010 Feb 11;114(5):2023-7

Authors: Paoli B, Pellarin R, Caflisch A

The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour.

Ecol Lett. 2010 Jan 21;

Authors: Kaiser-Bunbury CN, Muff S, Memmott J, Müller CB, Caflisch A

Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia.

Mol Microbiol. 2010 Feb 1;

Authors: Sonda S, Morf L, Bottova I, Baetschmann H, Rehrauer H, Caflisch A, Hakimi MA, Hehl AB

2D-IR Study of a Photoswitchable Isotope-Labeled alpha-Helix.

J Phys Chem B. 2010 Feb 18;

Authors: Backus EH, Bloem R, Donaldson PM, Ihalainen JA, Pfister R, Paoli B, Caflisch A, Hamm P

ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.

J Phys Chem B. 2009 Mar 12;113(10):3218-26

Authors: Muff S, Caflisch A

Predicting free energy changes using structural ensembles.

Nat Methods. 2009 Jan;6(1):3-4

Authors: Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA

Amyloid aggregation on lipid bilayers and its impact on membrane permeability.

J Mol Biol. 2009 Mar 27;387(2):407-15

Authors: Friedman R, Pellarin R, Caflisch A

Data management system for distributed virtual screening.

J Chem Inf Model. 2009 Jan;49(1):145-52

Authors: Zhou T, Caflisch A

Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking.

PLoS Negl Trop Dis. 2009;3(1):e356

Authors: Ekonomiuk D, Su XC, Ozawa K, Bodenreider C, Lim SP, Yin Z, Keller TH, Beer D, Patel V, Otting G, Caflisch A, Huang D

Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: a combined molecular dynamics and time-resolved infrared spectroscopy study.

J Phys Chem B. 2009 Apr 2;113(13):4435-42

Authors: Paoli B, Seeber M, Backus EH, Ihalainen JA, Hamm P, Caflisch A

9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation?

Protein Sci. 2009 Apr;18(4):792-800

Authors: Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A

Identification of the protein folding transition state from molecular dynamics trajectories.

J Chem Phys. 2009 Mar 28;130(12):125104

Authors: Muff S, Caflisch A

Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism.

Protein Sci. 2009 May;18(5):1003-11

Authors: Ekonomiuk D, Caflisch A

The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development.

PLoS One. 2009;4(4):e5335

Authors: Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, Caflisch A, Gruissem W, Köhler C, Hennig L

CHARMM: the biomolecular simulation program.

J Comput Chem. 2009 Jul 30;30(10):1545-614

Authors: Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M

Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring.

ChemMedChem. 2009 Aug;4(8):1317-26

Authors: Friedman R, Caflisch A

Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics.

J Med Chem. 2009 Aug 13;52(15):4860-8

Authors: Ekonomiuk D, Su XC, Ozawa K, Bodenreider C, Lim SP, Otting G, Huang D, Caflisch A

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease.

FEBS J. 2009 Aug;276(15):4244-55

Authors: Su XC, Ozawa K, Yagi H, Lim SP, Wen D, Ekonomiuk D, Huang D, Keller TH, Sonntag S, Caflisch A, Vasudevan SG, Otting G

A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease.

Anal Biochem. 2009 Dec 15;395(2):195-204

Authors: Bodenreider C, Beer D, Keller TH, Sonntag S, Wen D, Yap L, Yau YH, Shochat SG, Huang D, Zhou T, Caflisch A, Su XC, Ozawa K, Otting G, Vasudevan SG, Lescar J, Lim SP

How does a simplified-sequence protein fold?

Biophys J. 2009 Sep 16;97(6):1737-46

Authors: Guarnera E, Pellarin R, Caflisch A

Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4).

J Med Chem. 2009 Oct 22;52(20):6433-46

Authors: Lafleur K, Huang D, Zhou T, Caflisch A, Nevado C

Quantum Mechanical Methods for Drug Design.

Curr Top Med Chem. 2009 Nov 23;

Authors: Zhou T, Huang D, Caflisch A

On the orientation of the catalytic dyad in aspartic proteases.

Proteins. 2009 Dec 21;

Authors: Friedman R, Caflisch A

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein.

Proteins. 2008 Mar;70(4):1185-95

Authors: Muff S, Caflisch A

FACTS: Fast analytical continuum treatment of solvation.

J Comput Chem. 2008 Apr 15;29(5):701-15

Authors: Haberthür U, Caflisch A

Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments.

J Mol Biol. 2008 Jan 18;375(3):837-54

Authors: Interlandi G, Wetzel SK, Settanni G, Plückthun A, Caflisch A

Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core.

J Mol Biol. 2008 Mar 7;376(5):1282-304

Authors: Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A

Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model.

J Med Chem. 2008 Mar 13;51(5):1179-88

Authors: Kolb P, Huang D, Dey F, Caflisch A

Fragment-based de novo ligand design by multiobjective evolutionary optimization.

J Chem Inf Model. 2008 Mar;48(3):679-90

Authors: Dey F, Caflisch A

Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors.

Proteins. 2008 Oct;73(1):11-8

Authors: Kolb P, Kipouros CB, Huang D, Caflisch A

Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Apr;77(4 Pt 2):046112

Authors: Schuetz P, Caflisch A

Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis.

Proteins. 2008 Dec;73(4):814-27

Authors: Friedman R, Caflisch A

Is quantum mechanics necessary for predicting binding free energy?

J Med Chem. 2008 Jul 24;51(14):4280-8

Authors: Zhou T, Huang D, Caflisch A

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process.

J Phys Chem B. 2008 Jul 24;112(29):8701-14

Authors: Krivov SV, Muff S, Caflisch A, Karplus M

Alpha-Helix folding in the presence of structural constraints.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9588-93

Authors: Ihalainen JA, Paoli B, Muff S, Backus EH, Bredenbeck J, Woolley GA, Caflisch A, Hamm P

A double-headed cathepsin B inhibitor devoid of warhead.

Protein Sci. 2008 Dec;17(12):2145-55

Authors: Schenker P, Alfarano P, Kolb P, Caflisch A, Baici A

Multistep greedy algorithm identifies community structure in real-world and computer-generated networks.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Aug;78(2 Pt 2):026112

Authors: Schuetz P, Caflisch A

Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins.

Proteins. 2007 Jul 1;68(1):273-8

Authors: Tartaglia GG, Caflisch A

Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier.

FASEB J. 2007 Oct;21(12):3279-87

Authors: Gorfe AA, Caflisch A

Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form.

Thromb Haemost. 2007 Jun;97(6):890-8

Authors: Schroeder V, Vuissoz JM, Caflisch A, Kohler HP

The protonation state of the catalytic aspartates in plasmepsin II.

FEBS Lett. 2007 Aug 21;581(21):4120-4

Authors: Friedman R, Caflisch A

Wordom: a program for efficient analysis of molecular dynamics simulations.

Bioinformatics. 2007 Oct 1;23(19):2625-7

Authors: Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A

Pathways and intermediates of amyloid fibril formation.

J Mol Biol. 2007 Dec 7;374(4):917-24

Authors: Pellarin R, Guarnera E, Caflisch A

Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding.

Methods Mol Biol. 2007;350:225-49

Authors: Rao F, Settanni G, Caflisch A

Complex network analysis of free-energy landscapes.

Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1817-22

Authors: Gfeller D, De Los Rios P, Caflisch A, Rao F

Network and graph analyses of folding free energy surfaces.

Curr Opin Struct Biol. 2006 Feb;16(1):71-8

Authors: Caflisch A

Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations.

Proteins. 2006 Jul 1;64(1):178-92

Authors: Interlandi G, Settanni G, Caflisch A

In silico discovery of beta-secretase inhibitors.

J Am Chem Soc. 2006 Apr 26;128(16):5436-43

Authors: Huang D, Lüthi U, Kolb P, Cecchini M, Barberis A, Caflisch A

Interpreting the aggregation kinetics of amyloid peptides.

J Mol Biol. 2006 Jul 21;360(4):882-92

Authors: Pellarin R, Caflisch A

Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane.

Biophys J. 2006 Nov 1;91(9):3276-84

Authors: Seeber M, Fanelli F, Paci E, Caflisch A

Computational models for the prediction of polypeptide aggregation propensity.

Curr Opin Chem Biol. 2006 Oct;10(5):437-44

Authors: Caflisch A

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.

J Med Chem. 2006 Dec 14;49(25):7384-92

Authors: Kolb P, Caflisch A

A molecular dynamics approach to the structural characterization of amyloid aggregation.

J Mol Biol. 2006 Apr 7;357(4):1306-21

Authors: Cecchini M, Curcio R, Pappalardo M, Melki R, Caflisch A

Phi-value analysis by molecular dynamics simulations of reversible folding.

Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):628-33

Authors: Settanni G, Rao F, Caflisch A

Spontaneous formation of detergent micelles around the outer membrane protein OmpX.

Biophys J. 2005 May;88(5):3191-204

Authors: Böckmann RA, Caflisch A

Estimation of protein folding probability from equilibrium simulations.

J Chem Phys. 2005 May 8;122(18):184901

Authors: Rao F, Settanni G, Guarnera E, Caflisch A

Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations.

J Med Chem. 2005 Aug 11;48(16):5108-11

Authors: Huang D, Lüthi U, Kolb P, Edler K, Cecchini M, Audetat S, Barberis A, Caflisch A

Organism complexity anti-correlates with proteomic beta-aggregation propensity.

Protein Sci. 2005 Oct;14(10):2735-40

Authors: Tartaglia GG, Pellarin R, Cavalli A, Caflisch A

Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex.

Protein Sci. 2005 Oct;14(10):2499-514

Authors: Curcio R, Caflisch A, Paci E

Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences.

Protein Sci. 2005 Oct;14(10):2723-34

Authors: Tartaglia GG, Cavalli A, Pellarin R, Caflisch A

Functional plasticity in the substrate binding site of beta-secretase.

Structure. 2005 Oct;13(10):1487-98

Authors: Gorfe AA, Caflisch A

Local modularity measure for network clusterizations.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov;72(5 Pt 2):056107

Authors: Muff S, Rao F, Caflisch A

Automated docking of highly flexible ligands by genetic algorithms: a critical assessment.

J Comput Chem. 2004 Feb;25(3):412-22

Authors: Cecchini M, Kolb P, Majeux N, Caflisch A

The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis.

J Mol Recognit. 2004 Mar-Apr;17(2):120-31

Authors: Gorfe AA, Caflisch A, Jelesarov I

The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates.

Protein Sci. 2004 Jul;13(7):1939-41

Authors: Tartaglia GG, Cavalli A, Pellarin R, Caflisch A

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

J Mol Biol. 2004 Jun 25;340(1):67-79

Authors: Levy Y, Caflisch A, Onuchic JN, Wolynes PG

The protein folding network.

J Mol Biol. 2004 Sep 3;342(1):299-306

Authors: Rao F, Caflisch A

Protein folding: simple models for a complex process.

Structure. 2004 Oct;12(10):1750-2

Authors: Caflisch A

Efficient evaluation of binding free energy using continuum electrostatics solvation.

J Med Chem. 2004 Nov 4;47(23):5791-7

Authors: Huang D, Caflisch A

Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations.

J Am Chem Soc. 2004 Nov 24;126(46):15277-86

Authors: Gorfe AA, Pellarin R, Caflisch A

Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

Biophys J. 2004 Mar;86(3):1691-701

Authors: Settanni G, Gsponer J, Caflisch A

Replica exchange molecular dynamics simulations of amyloid peptide aggregation.

J Chem Phys. 2004 Dec 1;121(21):10748-56

Authors: Cecchini M, Rao F, Seeber M, Caflisch A

A sphere-based model for the electrostatics of globular proteins.

J Am Chem Soc. 2003 Apr 16;125(15):4600-8

Authors: Werner P, Caflisch A

The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35.

Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5154-9

Authors: Gsponer J, Haberthür U, Caflisch A

Analysis of the distributed computing approach applied to the folding of a small beta peptide.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8217-22

Authors: Paci E, Cavalli A, Vendruscolo M, Caflisch A

Fast protein folding on downhill energy landscape.

Protein Sci. 2003 Aug;12(8):1801-3

Authors: Cavalli A, Haberthür U, Paci E, Caflisch A

Folding for binding or binding for folding?

Trends Biotechnol. 2003 Oct;21(10):423-5

Authors: Caflisch A

Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution.

J Comput Chem. 2003 Nov 30;24(15):1936-49

Authors: Haberthür U, Majeux N, Werner P, Caflisch A

Replica exchange molecular dynamics simulations of reversible folding

Journal of Chemical Physics 119, 4035-4042, 2003.

Authors: Rao F and Caflisch A

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform

Third IEEE International Symposium on Cluster Computing and the Grid (CCGrid'03), 2003

Authors: Uk B. ,Taufer M. ,Stricker T. ,Settanni G. ,Cavalli A. , Caflisch A

Flexibility of Monomeric and Dimeric HIV-1 Protease

J. Phys. Chem. B, 107 (13), 3068 -3079, 2003.

Authors: Levy Y, Caflisch A

Evaluation of a fast implicit solvent model for molecular dynamics simulations.

Proteins. 2002 Jan 1;46(1):24-33

Authors: Ferrara P, Apostolakis J, Caflisch A

Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase.

Proteins. 2002 Jan 1;46(1):41-60

Authors: Gorfe AA, Ferrara P, Caflisch A, Marti DN, Bosshard HR, Jelesarov I

Weak temperature dependence of the free energy surface and folding pathways of structured peptides.

Proteins. 2002 May 15;47(3):305-14

Authors: Cavalli A, Ferrara P, Caflisch A

Molecular dynamics simulations of protein folding from the transition state.

Proc Natl Acad Sci U S A. 2002 May 14;99(10):6719-24

Authors: Gsponer J, Caflisch A

Performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM?

Parallel and Distributed Processing Symposium., Proceedings International, IPDPS 2002, Abstracts and CD-ROM

Authors: Taufer, M.; Perathoner, E.; Cavalli, A.; Caflisch, A.; Stricker, T.;

Efficient electrostatic solvation model for protein-fragment docking.

Proteins. 2001 Feb 1;42(2):256-68

Authors: Majeux N, Scarsi M, Caflisch A

Native topology or specific interactions: what is more important for protein folding?

J Mol Biol. 2001 Mar 2;306(4):837-50

Authors: Ferrara P, Caflisch A

Hydrophobicity and functionality maps of farnesyltransferase.

J Mol Graph Model. 2001;19(3-4):307-17, 380-7

Authors: Ahmed S, Majeux N, Caflisch A

Role of native topology investigated by multiple unfolding simulations of four SH3 domains.

J Mol Biol. 2001 May 25;309(1):285-98

Authors: Gsponer J, Caflisch A

Fragment-Based flexible ligand docking by evolutionary optimization.

Biol Chem. 2001 Sep;382(9):1365-72

Authors: Budin N, Majeux N, Caflisch A

Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations.

J Mol Graph Model. 2001;20(2):169-82

Authors: Gsponer J, Ferrara P, Caflisch A

An evolutionary approach for structure-based design of natural and non-natural peptidic ligands.

Comb Chem High Throughput Screen. 2001 Dec;4(8):661-73

Authors: Budin N, Ahmed S, Majeux N, Caflisch A

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study.

J Mol Biol. 2001 Nov 30;314(3):589-605

Authors: Paci E, Caflisch A, Plückthun A, Karplus M

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein.

Journal of Computational Chemistry (2001), 22(16), 1956-1970.

Authors: Budin, Nicolas; Majeux, Nicolas; Tenette-Souaille, Catherine; Caflisch, Amedeo

Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach.

J Comput Aided Mol Des. 2000 Feb;14(2):161-79

Authors: Caflisch A, Schramm HJ, Karplus M

Computer simulations of protein folding by targeted molecular dynamics.

Proteins. 2000 May 15;39(3):252-60

Authors: Ferrara P, Apostolakis J, Caflisch A

Folding simulations of a three-stranded antiparallel beta -sheet peptide.

Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10780-5

Authors: Ferrara P, Caflisch A

Free energy surface of the helical peptide Y(MEARA)6.

Journal of Physical Chemistry B (2000), 104(43), 10080-10086.

Authors: Hiltpold, Andre; Ferrara, Philippe; Gsponer, Joerg; Caflisch, Amedeo

Hydrophobicity Maps and Docking of Molecular Fragments with Solvation.

PERSPECTIVES IN DRUG DISCOVERY AND DESIGN 20 : 145 2000

Authors: Majeux N, Scarsi M, Tenette-Souaille C and Caflisch A

Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations

J. Phys. Chem. B, 104 (20), 5000 -5010, 2000.

Authors: Ferrara P, Apostolakis J, and Caflisch A

Targeted molecular dynamics simulations of protein unfolding.

J. Phys. Chem. B 104, 4511-4518, 2000

Authors: Ferrara, P; Apostolakis, J; Caflisch, A

Structural details of urea binding to barnase: a molecular dynamics analysis.

Structure. 1999 May;7(5):477-88

Authors: Caflisch A, Karplus M

Computational ligand design.

Comb Chem High Throughput Screen. 1999 Apr;2(2):91-104

Authors: Apostolakis J, Caflisch A

Exhaustive docking of molecular fragments with electrostatic solvation.

Proteins. 1999 Oct 1;37(1):88-105

Authors: Majeux N, Scarsi M, Apostolakis J, Ehrhardt C, Caflisch A

Hydrophobicity at the surface of proteins.

Proteins. 1999 Dec 1;37(4):565-75

Authors: Scarsi M, Majeux N, Caflisch A

Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations.

J Mol Graph Model. 1999 Feb;17(1):19-27

Authors: Galzitskaya O, Caflisch A

Comment on the validation of continuum electrostatics models

J. Comput. Chem. 20, 1533-1536, 1999

Authors: Scarsi M, Caflisch A

Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water

J. Chem. Phys. 110, 2099-2108, 1999

Authors: Apostolakis, J; Ferrara, P; Caflisch, A

Computer-Aided Design of Thrombin Inhibitors.

News Physiol Sci. 1998 Aug;13():182-189

Authors: Caflisch A, Wälchli R, Ehrhardt C

Docking small ligands in flexible binding sites

J. Comput. Chem. 19, 21-37, 1998

Authors: Apostolakis, J; Pluckthun, A; Caflisch, A

Comparison of a GB solvation model with explicit solvent simulations: Potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane

J. Phys. Chem. B 102, 3637-3641, 1998

Authors: Scarsi, M; Apostolakis, J; Caflisch, A

Continuum electrostatic energies of macromolecules in aqueous solutions

J. Phys. Chem. A 101, 8098-8106, 1997

Authors: Scarsi, M; Apostolakis, J; Caflisch, A

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex

J. Comput. Chem. 18, 723-743, 1997

Authors: Caflisch, A; Fischer, S; Karplus, M

Computational combinatorial ligand design: application to human alpha-thrombin.

J Comput Aided Mol Des. 1996 Oct;10(5):372-96

Authors: Caflisch A

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.

J Mol Biol. 1995 Oct 6;252(5):672-708

Authors: Caflisch A, Karplus M

Computational combinatorial chemistry for de novo ligand design: Review and assessment

Perspectives in Drug Discovery and Design 3, 51-84, 1995

Authors: Caflisch, A; Karplus, M

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.

Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1746-50

Authors: Caflisch A, Karplus M

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase.

J Med Chem. 1993 Jul 23;36(15):2142-67

Authors: Caflisch A, Miranker A, Karplus M

Monte Carlo docking of oligopeptides to proteins.

Proteins. 1992 Jul;13(3):223-30

Authors: Caflisch A, Niederer P, Anliker M

Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space.

Proteins. 1992 Sep;14(1):102-9

Authors: Caflisch A, Niederer P, Anliker M