Why relevant chemical information cannot be exchanged without disclosing structures.

abstract：:In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screenin...

journal_title：Journal of computer-aided molecular design

authors： Nikitina N,Ivashko E,Tchernykh A

更新日期：2018-02-01 00:00:00

abstract：:Moment descriptors of the molecular charge and mass distributions are investigated within the context of molecular similarity. Euclidean distances in the moment descriptor space are shown to yield molecular proximities in accord with chemical intuition for a substituted [(4-phenylpiperazinyl)-methyl] benzamide series ...

journal_title：Journal of computer-aided molecular design

authors： Silverman BD,Pitman MC,Platt DE,Rigoutsos I

更新日期：1998-11-01 00:00:00

abstract：:A Comparative Molecular Field Analysis (CoMFA) and an interaction energy-based method were applied on a database holding the 3D structures of 29 thrombin-inhibitor complexes. Several parameters were optimized in both methods in order to obtain the best correlation between theoretical and experimentally determined bind...

journal_title：Journal of computer-aided molecular design

authors： Bursi R,Grootenhuis PD

更新日期：1999-05-01 00:00:00

abstract：:In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters hig...

journal_title：Journal of computer-aided molecular design

authors： Nascimento ÉCM,Oliva M,Andrés J

更新日期：2018-05-01 00:00:00

abstract：:Manifold representations of rotational/translational motion and conformational space of a ligand were previously shown to be effective for local energy optimization. In this paper we report the development of the Monte-Carlo energy minimization approach (MCM), which uses the same manifold representation. The approach ...

journal_title：Journal of computer-aided molecular design

authors： Ignatov M,Liu C,Alekseenko A,Sun Z,Padhorny D,Kotelnikov S,Kazennov A,Grebenkin I,Kholodov Y,Kolosvari I,Perez A,Dill K,Kozakov D

更新日期：2019-01-01 00:00:00

abstract：:4-(Phenylamino)-pyrrolo[2,1-f][1,2,4]triazines have been discovered as inhibitors of p38alpha. Experimental assays have proven that the configuration of alpha-Me-benzyl connected with amide at C6 is essential for the binding affinity. The S-configured inhibitor (11j) displays 80 times more potency than the R-configure...

journal_title：Journal of computer-aided molecular design

authors： Chen Q,Cui W,Ji M

更新日期：2009-10-01 00:00:00

abstract：:R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central activ...

journal_title：Journal of computer-aided molecular design

authors： Alonso H,Gillies MB,Cummins PL,Bliznyuk AA,Gready JE

更新日期：2005-03-01 00:00:00

abstract：:We used blind predictions of the 47 hydration free energies in the SAMPL4 challenge to test multiple partial charge models in the context of explicit solvent free energy simulations with the general AMBER force field. One of the partial charge models, IPolQ-Mod, is a fast continuum solvent-based implementation of the ...

journal_title：Journal of computer-aided molecular design

authors： Muddana HS,Sapra NV,Fenley AT,Gilson MK

更新日期：2014-03-01 00:00:00

abstract：:Chemical space networks (CSNs) have recently been introduced as an alternative to other coordinate-free and coordinate-based chemical space representations. In CSNs, nodes represent compounds and edges pairwise similarity relationships. In addition, nodes are annotated with compound property information such as biolog...

journal_title：Journal of computer-aided molecular design

authors： Zhang B,Vogt M,Maggiora GM,Bajorath J

更新日期：2015-10-01 00:00:00

abstract：:In the 1960s, the kappa statistic was introduced for the estimation of chance agreement in inter- and intra-rater reliability studies. The kappa statistic was strongly pushed by the medical field where it could be successfully applied via analyzing diagnoses of identical patient groups. Kappa is well suited for classi...

journal_title：Journal of computer-aided molecular design

authors： Czodrowski P

更新日期：2014-11-01 00:00:00

abstract：:Inducible, microsomal prostaglandin E synthase 1 (mPGES-1), the terminal enzyme in the prostaglandin (PG) biosynthetic pathway, constitutes a promising therapeutic target for the development of new anti-inflammatory drugs. To elucidate structure-function relationships and to enable structure-based design, an mPGES-1 h...

journal_title：Journal of computer-aided molecular design

authors： Xing L,Kurumbail RG,Frazier RB,Davies MS,Fujiwara H,Weinberg RA,Gierse JK,Caspers N,Carter JS,McDonald JJ,Moore WM,Vazquez ML

更新日期：2009-01-01 00:00:00

abstract：:Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze da...

journal_title：Journal of computer-aided molecular design

authors： Raschka S,Wolf AJ,Bemister-Buffington J,Kuhn LA

更新日期：2018-04-01 00:00:00

abstract：:A new method is presented for the calculation of the Molecular Electrostatic Potential (MEP) in large systems. Based on the mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach, the method assumes both a quantum and classical description for the molecule, and the calculation of the MEP in the space surrounding...

journal_title：Journal of computer-aided molecular design

authors： Hernández B,Luque FJ,Orozco M

更新日期：2000-05-01 00:00:00

abstract：:The complex of adenylate kinase with its transition-state inhibitor has been studied by molecular dynamics simulations in water and in vacuum environments with the GROMOS force field over a period of 300 ps. The adenylate kinase, a member of the nucleotide-binding protein family, was exemplarily chosen for the inspect...

journal_title：Journal of computer-aided molecular design

authors： Kern P,Brunne RM,Folkers G

更新日期：1994-08-01 00:00:00

abstract：:Electrostatic potential complementarity between ligands and their receptor sites is evaluated by the superposition of the electrostatic potential, generated by the receptor, onto the ligand potential over the ligand van der Waals surface. We would like to examine which structural factors generate this pattern of super...

journal_title：Journal of computer-aided molecular design

authors： Chau PL,Dean PM

更新日期：1994-10-01 00:00:00

abstract：:Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy ...

journal_title：Journal of computer-aided molecular design

authors： Chaudhari R,Heim AJ,Li Z

更新日期：2015-05-01 00:00:00

abstract：:The mounting evidences have shown that signal transducer and activator of transcription 3 (Stat3) is a critical target for cancer therapy. Recently, we developed a G-quartet oligonucleotide T40214 as a novel and potent Stat3 inhibitor. T40214 specifically inhibited DNA-binding activity of Stat3 and significantly suppr...

journal_title：Journal of computer-aided molecular design

authors： Zhu Q,Jing N

更新日期：2007-10-01 00:00:00

abstract：:Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more ...

journal_title：Journal of computer-aided molecular design

authors： Reid D,Sadjad BS,Zsoldos Z,Simon A

更新日期：2008-06-01 00:00:00

abstract：:In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously. ...

journal_title：Journal of computer-aided molecular design

authors： Chau PL,Dean PM

更新日期：1992-08-01 00:00:00

abstract：:A three-dimensional quantitative spectrometric data-activity relationship (3D-QSDAR) modeling technique which uses NMR spectral and structural information that is combined in a 3D-connectivity matrix has been developed. A 3D-connectivity matrix was built by displaying all possible assigned carbon NMR chemical shifts, ...

journal_title：Journal of computer-aided molecular design

authors： Beger RD,Buzatu DA,Wilkes JG

更新日期：2002-10-01 00:00:00

abstract：:We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken f...

journal_title：Journal of computer-aided molecular design

authors： Ozrin VD,Subbotin MV,Nikitin SM

更新日期：2004-04-01 00:00:00

abstract：:Overexpression of Bcl-2 and Bcl-xL proteins, both inhibitors of apoptosis or programmed cell death, is related to the generation and development of several types of cancer as well as to an elevated resistance to chemotherapeutic treatments. Given that synthetic peptide fragments of the BH3 domain are capable to bind t...

journal_title：Journal of computer-aided molecular design

authors： Pinto M,Perez JJ,Rubio-Martinez J

更新日期：2004-01-01 00:00:00

abstract：:Computational prediction of the effects of residue changes on peptide-protein binding affinities, followed by experimental testing of the top predicted binders, is an efficient strategy for the rational structure-based design of peptide inhibitors. In this study we apply this approach to the discovery of competitive a...

journal_title：Journal of computer-aided molecular design

authors： Te JA,Dong M,Miller LJ,Bordner AJ

更新日期：2012-07-01 00:00:00

abstract：:To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the...

journal_title：Journal of computer-aided molecular design

authors： Perryman AL,Santiago DN,Forli S,Martins DS,Olson AJ

更新日期：2014-04-01 00:00:00

abstract：:The CASE (Computer Automated Structure Evaluation) program, with the aid of a geometry index for discriminating cis and trans isomers, has been used to study a set of retinoids tested for teratogenicity in hamsters. CASE identified 8 fragments, the most important representing the non-polar terminus of a retinoid with ...

journal_title：Journal of computer-aided molecular design

authors： Klopman G,Dimayuga ML

更新日期：1990-06-01 00:00:00

abstract：:The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomer...

journal_title：Journal of computer-aided molecular design

authors： Cruz-Cabeza AJ,Schreyer A,Pitt WR

更新日期：2010-06-01 00:00:00

abstract：:Quantitative Structure-Activity Relationship (QSAR) models are critical in various areas of drug discovery, for example in lead optimisation and virtual screening. Recently, the need for models that are not only predictive but also interpretable has been highlighted. In this paper, a new methodology is proposed to bui...

journal_title：Journal of computer-aided molecular design

authors： Cardoso-Silva J,Papageorgiou LG,Tsoka S

更新日期：2019-09-01 00:00:00

abstract：:Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of t...

journal_title：Journal of computer-aided molecular design

authors： Padhorny D,Hall DR,Mirzaei H,Mamonov AB,Moghadasi M,Alekseenko A,Beglov D,Kozakov D

更新日期：2018-01-01 00:00:00

abstract：:To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge valu...

journal_title：Journal of computer-aided molecular design

authors： Leherte L,Vercauteren DP

更新日期：2011-10-01 00:00:00

abstract：:A method is suggested to calculate improved entropies within the MM/PBSA approach (molecular mechanics combined with Poisson-Boltzmann and surface area calculations) to estimate protein-ligand binding affinities. In the conventional approach, the protein is truncated outside ~8 A from the ligand. This system is freely...

journal_title：Journal of computer-aided molecular design

authors： Kongsted J,Ryde U

更新日期：2009-02-01 00:00:00