1. 2017
  2. 2016
  3. 2015
  4. 2014
  5. 2013
  6. 2012
  7. 2011
  8. 2010
  9. 2009
  10. 2008
  11. 2007
  12. 2006
  13. 2005
  14. 2004
  15. 2003
  16. 2002
  17. 2001
  18. 2000
  19. 1999
  20. 1998
  21. 1997
  22. 1996
  23. 1995
  24. 1994
  25. 1993
  26. 1992

Peer reviewed articles and book chapters

2017 (7)

N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment

Sci Rep. 2017 Feb;7:42108

Authors: Ghayor C., Gjoksi B., Dong J., Siegenthaler B., Caflisch A., Weber F.E.

Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain

Bioorg. Med. Chem. Lett. June 2017: 27.11, 2472-2478.

Spiliotopoulos D., Zhu J., Wamhoff E.C., Deerain N., Marchand J.R., Aretz J., Rademacher C., Caflisch A.

Discovery of BAZ2A Bromodomain Ligands

Eur J Med Chem. 2017 Aug 12;139:564-572.

Authors: Spiliotopoulos D., Wamhoff E.C., Lolli G., Rademacher C., Caflisch A.

Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking.

J. Chem. Inf. Model., Just Accepted Manuscript

Authors: Marchand JR, Dalle Vedove A, Lolli G, Caflisch A

The ATAD2 Bromodomain Binds Different Acetylation Marks on the Histone H4 in Similar Fuzzy Complexes.

J Biol Chem. 2017 Aug 10. [Epub ahead of print]

Authors: Langini C, Caflisch A, Vitalis A.

Reducing the Flexibility of Type II Dehydroquinase Enzyme for Inhibition - A Fragment-Based Approach and Molecular Dynamics Simulation Study.

ChemMedChem. 2017 Aug 9. [Epub ahead of print]

Authors: Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, Gonzalez-Bello C.

Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip

J Chem Theory Comput 2017 Oct 10;13(10):5117-5130

Authors: Bacci M, Vymětal J, Mihajlovic M, Caflisch A, Vitalis A.

2016 (14) top

Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain.

J Med Chem. 2016 Feb 25;59(4):1350-6

Authors: Unzue A, Xu M, Dong J, Wiedmer L, Spiliotopoulos D, Caflisch A, Nevado C

Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics.

J Med Chem. 2016 Feb 25;59(4):1340-9

Authors: Xu M, Unzue A, Dong J, Spiliotopoulos D, Nevado C, Caflisch A

Protein structural memory influences ligand binding mode(s) and unbinding rates.

J Chem Theory Comput. 2016 Jan 22;

Authors: Xu M, Caflisch A, Hamm P

Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation.

Eur J Med Chem. 2016 Feb 2;112:347-366

Authors: Unzue A, Lafleur K, Zhao H, Zhou T, Dong J, Kolb P, Liebl J, Zahler S, Caflisch A, Nevado C

Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein.

Cell Rep. 2016 Feb 24;

Authors: Ben Halima S, Mishra S, Raja KM, Willem M, Baici A, Simons K, Brüstle O, Koch P, Haass C, Caflisch A, Rajendran L

High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-ray crystallography.

ACS Chem Biol. 2016 Mar 4;

Authors: Lolli G, Caflisch A

Data publication with the structural biology data grid supports live analysis.

Nat Commun. 2016;7:10882

Authors: Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P

The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains.

J Med Chem. 2016 Apr 14;59(7):3087-97

Authors: Unzue A, Zhao H, Lolli G, Dong J, Zhu J, Zechner M, Dolbois A, Caflisch A, Nevado C

Twenty crystal structures of bromodomain and PHD finger containing protein 1 (BRPF1)/ligand complexes reveal conserved binding motifs and rare interactions.

J Med Chem. 2016 May 11;

Authors: Zhu J, Caflisch A

A Small-Molecule Inhibitor of Lin28.

ACS Chem Biol. 2016 Oct 21;11(10):2773-2781

Authors: Roos M, Pradère U, Ngondo RP, Behera A, Allegrini S, Civenni G, Zagalak JA, Marchand JR, Menzi M, Towbin H, Scheuermann J, Neri D, Caflisch A, Catapano CV, Ciaudo C, Hall J

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.

J Mol Biol. 2016 Sep 21;

Authors: Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Plückthun A

Derivatives of 3-amino-2-methylpyridine as BAZ2B Bromodomain Ligands: in silico Discovery and in crystallo Validation.

J Med Chem. 2016 Oct 12;

Authors: Marchand JR, Lolli G, Caflisch A

Fragment-based in silico screening of bromodomain ligands.

Drug Discov Today Technol. 2016 Mar;19:81-90

Authors: Spiliotopoulos D, Caflisch A

Dynamic microfluidic control of supramolecular peptide self-assembly.

Nat Commun. 2016 Oct 25;7:13190

Authors: Arnon ZA, Vitalis A, Levin A, Michaels TC, Caflisch A, Knowles TP, Adler-Abramovich L, Gazit E

2015 (12) top

Molecular dynamics in drug design.

Eur J Med Chem. 2015 Feb 16;91:4-14

Authors: Zhao H, Caflisch A

A molecular simulation protocol to avoid sampling redundancy and discover new states.

Biochim Biophys Acta. 2015 May;1850(5):889-902

Authors: Bacci M, Vitalis A, Caflisch A

Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases.

ACS Med Chem Lett. 2015 Jan 8;6(1):79-83

Authors: Dong J, Zhao H, Zhou T, Spiliotopoulos D, Rajendran C, Li XD, Huang D, Caflisch A

Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein.

J Am Chem Soc. 2015 Mar 4;137(8):2948-57

Authors: Huang D, Caflisch A

Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations

Biochemistry. 2015, 54 (3), pp 711–721

Authors: Müller C S, Knehans T, Davydov D R, Bounds P L, von Mandach U, Halpert J R, Caflisch A, Koppenol W H

A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein.

J Mol Biol. 2015 May 22;427(10):1916-33

Authors: Ewald C, Christen MT, Watson RP, Mihajlovic M, Zhou T, Honegger A, Plückthun A, Caflisch A, Zerbe O

Peptide Binding to a PDZ Domain by Electrostatic Steering via Non-Native Salt Bridges

Biophys J. 2015

Authors:Bloechliger N, Xu M., Caflisch A

Current kinase inhibitors cover a tiny fraction of fragment space.

Bioorg Med Chem Lett. 2015 Jun 1;25(11):2372-6

Authors: Zhao H, Caflisch A

Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif.

ChemMedChem. 2015 Aug;10(8):1327-33

Authors: Marchand JR, Caflisch A

Structure-based drug design identifies polythiophenes as antiprion compounds.

Sci Transl Med. 2015 Aug 5;7(299):299ra123

Authors: Herrmann US, Schütz AK, Shirani H, Huang D, Saban D, Nuvolone M, Li B, Ballmer B, Åslund AK, Mason JJ, Rushing E, Budka H, Nyström S, Hammarström P, Böckmann A, Caflisch A, Meier BH, Nilsson KP, Hornemann S, Aguzzi A

Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations.

J Chem Theory Comput. 2015 Nov 10;11(11):5481-92

Authors: Blöchliger N, Caflisch A, Vitalis A

The roles of the conserved tyrosine in the β2-α2 loop of the prion protein.

Prion. 2015;9(6):412-9

Authors: Huang D, Caflisch A

2014 (14) top

Structured water molecules in the binding site of bromodomains can be displaced by cosolvent.

ChemMedChem. 2014 Mar;9(3):573-9

Authors: Huang D, Rossini E, Steiner S, Caflisch A

Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348).

Leukemia. 2014 Feb;28(2):404-7

Authors: Zhou T, Georgeon S, Moser R, Moore DJ, Caflisch A, Hantschel O

Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study.

Proteins. 2014 Mar;82(3):399-404

Authors: Friedman R, Caflisch A

Equilibrium sampling approach to the interpretation of electron density maps.

Structure. 2014 Jan 7;22(1):156-67

Authors: Vitalis A, Caflisch A

Experimental and computational study of BODIPY dye-labeled cavitand dynamics.

J Am Chem Soc. 2014 Feb 12;136(6):2441-9

Authors: Pochorovski I, Knehans T, Nettels D, Müller AM, Schweizer WB, Caflisch A, Schuler B, Diederich F

A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods.

Nat Commun. 2014;5:3287

Authors: Novinec M, Korenč M, Caflisch A, Ranganathan R, Lenarčič B, Baici A

Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk.

Bioorg Med Chem Lett. 2014 Mar 15;24(6):1523-7

Authors: Zhao H, Caflisch A

ALMOST: an all atom molecular simulation toolkit for protein structure determination.

J Comput Chem. 2014 May 30;35(14):1101-5

Authors: Fu B, Sahakyan AB, Camilloni C, Tartaglia GG, Paci E, Caflisch A, Vendruscolo M, Cavalli A

Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking.

Bioorg Med Chem Lett. 2014 Jun 1;24(11):2493-6

Authors: Zhao H, Gartenmann L, Dong J, Spiliotopoulos D, Caflisch A

Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine.

Isr J Chem 2014 Apr 8;

Authors: Spiliotopoulos D, Caflisch A

Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure.

Structure. 2014 Jul 8;22(7):985-95

Authors: Watson RP, Christen MT, Ewald C, Bumbak F, Reichen C, Mihajlovic M, Schmidt E, Güntert P, Caflisch A, Plückthun A, Zerbe O

Pyrrolo[3,2-b]quinoxaline derivatives as types I1/2 and II Eph tyrosine kinase inhibitors: structure-based design, synthesis, and in vivo validation.

J Med Chem. 2014 Aug 14;57(15):6834-44

Authors: Unzue A, Dong J, Lafleur K, Zhao H, Frugier E, Caflisch A, Nevado C

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

J Chem Inf Model. 2014 Sep 22;54(9):2612-20

Authors: Pevzner Y, Frugier E, Schalk V, Caflisch A, Woodcock HL

High-resolution visualisation of the States and pathways sampled in molecular dynamics simulations.

Sci Rep. 2014;4:6264

Authors: Blöchliger N, Vitalis A, Caflisch A

2013 (10) top

Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography.

J Med Chem. 2013 Jan 10;56(1):84-96

Authors: Lafleur K, Dong J, Huang D, Caflisch A, Nevado C

Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation.

J Phys Chem B. 2013 Feb 14;117(6):1780-9

Authors: Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A

Carnosine inhibits Aβ(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster.

Chembiochem. 2013 Mar 18;14(5):583-92

Authors: Attanasio F, Convertino M, Magno A, Caflisch A, Corazza A, Haridas H, Esposito G, Cataldo S, Pignataro B, Milardi D, Rizzarelli E

Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases.

Nat Struct Mol Biol. 2013 Apr;20(4):502-7

Authors: Rosenthal F, Feijs KL, Frugier E, Bonalli M, Forst AH, Imhof R, Winkler HC, Fischer D, Caflisch A, Hassa PO, Lüscher B, Hottiger MO

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.

J Phys Chem B. 2013 May 23;117(20):6092-105

Authors: Kalgin IV, Caflisch A, Chekmarev SF, Karplus M

Does bromodomain flexibility influence histone recognition?

FEBS Lett. 2013 Jul 11;587(14):2158-63

Authors: Steiner S, Magno A, Huang D, Caflisch A

Kinetic response of a photoperturbed allosteric protein.

Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11725-30

Authors: Buchli B, Waldauer SA, Walser R, Donten ML, Pfister R, Blöchliger N, Steiner S, Caflisch A, Zerbe O, Hamm P

Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics.

Bioorg Med Chem Lett. 2013 Oct 15;23(20):5721-6

Authors: Zhao H, Caflisch A

A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems

Comput Phys Comm, 184, 11, 2013, 2446–2453

Authors: Blöchliger N, Vitalis A, Caflisch A

Mechanism and Kinetics of Acetyl-Lysine Binding to Bromodomains

J Chem Theory Comput, 2013, 9 (9), pp 4225–4232

Authors: Magno A, Steiner S, Caflisch A

2012 (15) top

50 Years of Lifson–Roig Models: Application to Molecular Simulation Data

J. Chem. Theory Comput. 8, 363-373, 2012

Authors:Vitalis A, Caflisch A

Complexity in Protein Folding: Simulation Meets Experiment

Current Physical Chemistry, 2012, 2, 4-11

Authors: Caflisch A and Hamm P

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

J. Chem. Theory Comput. 8, 1108-1120, 2012

Authors:Vitalis A, Caflisch A

Ultrametricity in Protein Folding Dynamics

J. Chem. Theory Comput. 8, 1580-1588, 2012

Authors:Scalco R, Caflisch A

Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model

book chapter in "Computational Modeling of Biological Systems: From Molecules to Pathways", Nikolay v. Dokholyan editor, London, 191-214, 2012

Authors: Magno A, Pellarin R, Caflisch A

Inhibition of interdomain motion in g-actin by the natural product latrunculin: a molecular dynamics study.

Proteins. 2012 Aug;80(8):1998-2008

Authors: Rennebaum S, Caflisch A

How Does Darunavir Prevent HIV-1 Protease Dimerization?

J. Chem. Theory and Comput. 8, 1786-1794, 2012

Authors: Huang D, Caflisch A

Free Energy Guided Sampling

J. Chem. Theory Comput. 2012, 8 (6), pp 2134–2140

Authors: Zhou T, Caflisch A

Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria.

Nat Chem Biol. 2012 Aug;8(8):701-6

Authors: Adler-Abramovich L, Vaks L, Carny O, Trudler D, Magno A, Caflisch A, Frenkel D, Gazit E

Photocontrol of reversible amyloid formation with a minimal-design peptide.

J Phys Chem B. 2012 Aug 2;116(30):8961-73

Authors: Waldauer SA, Hassan S, Paoli B, Donaldson PM, Pfister R, Hamm P, Caflisch A, Pellarin R

Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy.

Protein Sci. 2012 Sep;21(9):1298-314

Authors: Alfarano P, Varadamsetty G, Ewald C, Parmeggiani F, Pellarin R, Zerbe O, Plückthun A, Caflisch A

Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics.

ChemMedChem. 2012 Nov;7(11):1983-90

Authors: Zhao H, Huang D, Caflisch A

Peptide binding to the PDZ3 domain by conformational selection.

Proteins. 2012 Nov;80(11):2562-72

Authors: Steiner S, Caflisch A

Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics

ACS Med. Chem. Lett., 2012, 3 (10), pp 834–838

Authors: Zhao H, Dong, J, Lafleur K, Nevado C, Caflisch A

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

J. Chem. Theory Comput., 2012, 8 (8), pp 2930–2937

Authors: Zhou T, Caflisch A

2011 (11) top

The free energy landscape of small molecule unbinding.

PLoS Comput Biol. 2011 Feb;7(2):e1002002

Authors: Huang D, Caflisch A

Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces.

J Comput Chem. 2011 Apr 30;32(6):1183-94

Authors: Seeber M, Felline A, Raimondi F, Muff S, Friedman R, Rao F, Caflisch A, Fanelli F

Equilibrium distribution from distributed computing (simulations of protein folding).

J Phys Chem B. 2011 May 19;115(19):6358-65

Authors: Scalco R, Caflisch A

Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations.

ChemMedChem. 2011 Sep 5;6(9):1578-80

Authors: Huang D, Caflisch A

In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):842-50

Authors: Ganesan R, Jelakovic S, Mittl PR, Caflisch A, Grütter MG

Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue.

ACS Chem Biol. 2011 Nov 18;6(11):1265-76

Authors: Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E

Dynamics in the active site of β-secretase: a network analysis of atomistic simulations.

Biochemistry. 2011 Nov 1;50(43):9328-39

Authors: Mishra S, Caflisch A

Delineation of folding pathways of a β-sheet miniprotein.

J Phys Chem B. 2011 Nov 10;115(44):13065-74

Authors: Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C

Disordered binding of small molecules to Aβ(12-28).

J Biol Chem. 2011 Dec 2;286(48):41578-88

Authors: Convertino M, Vitalis A, Caflisch A

Surfactant effects on amyloid aggregation kinetics.

J Mol Biol. 2011 Nov 25;414(2):303-12

Authors: Friedman R, Caflisch A

Hydrogen bonding penalty upon ligand binding.

PLoS One. 2011;6(6):e19923

Authors: Zhao H, Huang D

2010 (20) top

Library screening by fragment-based docking.

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

Authors: Huang D, Caflisch A

Quantum mechanical methods for drug design.

Curr Top Med Chem. 2010;10(1):33-45

Authors: Zhou T, 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 Apr;13(4):442-52

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

On the orientation of the catalytic dyad in aspartic proteases.

Proteins. 2010 May 1;78(6):1575-82

Authors: Friedman R, Caflisch A

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

Mol Microbiol. 2010 Apr;76(1):48-67

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 Mar 18;114(10):3735-40

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

Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein.

J Phys Chem B. 2010 May 27;114(20):6979-89

Authors: Qi B, Muff S, Caflisch A, Dinner AR

PARP1 ADP-ribosylates lysine residues of the core histone tails.

Nucleic Acids Res. 2010 Oct 1;38(19):6350-62

Authors: Messner S, Altmeyer M, Zhao H, Pozivil A, Roschitzki B, Gehrig P, Rutishauser D, Huang D, Caflisch A, Hottiger MO

High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors.

ChemMedChem. 2010 Jul 5;5(7):1007-14

Authors: Zhou T, Caflisch A

Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor.

PLoS One. 2010;5(6):e11101

Authors: Scherzer-Attali R, Pellarin R, Convertino M, Frydman-Marom A, Egoz-Matia N, Peled S, Levy-Sakin M, Shalev DE, Caflisch A, Gazit E, Segal D

Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation.

J Mol Biol. 2010 Oct 15;403(1):148-65

Authors: Vitalis A, Caflisch A

Complementing ultrafast shape recognition with an optical isomerism descriptor.

J Mol Graph Model. 2010 Nov;29(3):443-9

Authors: Zhou T, Lafleur K, Caflisch A

Amyloid fibril polymorphism is under kinetic control.

J Am Chem Soc. 2010 Oct 27;132(42):14960-70

Authors: Pellarin R, Schuetz P, Guarnera E, Caflisch A

Crowding Effects on Amyloid Aggregation Kinetics

J. Phys. Chem. Lett., 2010, 1, 3027–3032

Authors: Magno A, Caflisch A, Pellarin R

Free energy surfaces from single-distance information.

J Phys Chem B. 2010 Nov 25;114(46):15227-35

Authors: Schuetz P, Wuttke R, Schuler B, Caflisch A

A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering.

Plant Physiol. 2010 Dec;154(4):1633-45

Authors: Exner V, Alexandre C, Rosenfeldt G, Alfarano P, Nater M, Caflisch A, Gruissem W, Batschauer A, Hennig L

Fast Analytical Continuum Treatments of Solvation

Modeling Solvent Environments: Applications to Simulations of Biomolecules

Authors:Marchand F, Caflisch A

2009 (17) top

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

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

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

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

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

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

Authors: Friedman R, Caflisch A

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

2008 (14) top

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

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

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

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

2007 (8) top

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

2006 (8) top

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

2005 (11) top

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

Molecular dynamics simulations to study protein folding and unfolding.

J. Buchner, T. Kiefhaber, editors, Protein Folding Handbook, 2005.

Authors: Caflisch A and Paci E

Fragment-based high-throughput docking.

B. Shoichet and J. Alvarez, editors, Virtual Screening, 2005.

Authors: Kolb P, Cecchini M, Huang D and Caflisch A

2004 (10) top

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

2003 (9) top

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

Flexibility of Monomeric and Dimeric HIV-1 Protease

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

Authors: Levy Y, 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

2002 (5) top

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.;

2001 (10) top

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

Structure-Based Ligand Design by a Build-Up Approach and Genetic Algorithm Search in Conformational Space

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

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

Fast Continuum Electrostatics Methods for Structure-Based Ligand Docking.

A. K. Ghose and V. N. Viswanadhan, editors, Combinatorial Library Design and Evaluation, 197-231, New York, Marcel Dekker Inc., 2001.

Authors: Tenette-Souaille C. , Budin N. , Majeux N. and Caflisch A.

2000 (7) top

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 A, Ferrara P, Gsponer J, Caflisch A

Hydrophobicity Maps and Docking of Molecular Fragments with Solvation.


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

1999 (7) top

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

1998 (3) top

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

1997 (3) top

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

Structure-Based Combinatorial Ligand Design.

P. Veerapandian, editor, Structure-Based Drug Design, 541-558, New York, Marcel Dekker Inc., 1997.

Authors: Caflisch A. and Ehrhardt C.

1996 (1) top

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

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

Authors: Caflisch A

1995 (3) top

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

Protein Dynamics: From the Native to the Unfolded State and Back Again.

A. Pullman et al., editors, Modelling of Biomolecular Structures and Mechanisms, 69--84, Kluwer Academic Publishers, 1995.

Authors: Karplus M. , Caflisch A. , Sali A. , and Shakhnovich E.

1994 (2) top

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

Molecular Dynamics Studies of Protein and Peptide Folding and Unfolding.

K. M. Merz Jr. and S. M. LeGrand, editors, The Protein Folding Problem and Tertiary Structure Prediction, 193--230, Birkhaeuser, Boston, 1994.

Authors: Caflisch A. and Karplus M.

1993 (1) top

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

1992 (2) top

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